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View Code? Open in Web Editor NEWMesh generation for SeisSol
License: BSD 3-Clause "New" or "Revised" License
pumgen's Issues
Failed in making Velocity aware mesh using PUMGEN
Describe the bug
I applied the <!-- VelocityAwareMeshing--> in the pumgen xml but failed to generate mesh following the velocity structure (both 1D material and 3D material case.
Expected behavior
Expect to see refinement on the meshing following the material file.
To Reproduce
Steps to reproduce the behavior:
Pumgen: /import/freenas-m-05-seissol/public2022/packages/PUMGen_sim10/build/pumgen
Simmodeler: SimModeler 8.0
Machine: Exception
Module loaded:
Currently Loaded Modulefiles:
1) mpi/2021.11
2) mpi.intel/2024
3) libpciaccess/0.17-gcc-12.2.0-foegz6x
4) libiconv/1.17-gcc-12.2.0-pztn24l
5) xz/5.4.1-gcc-12.2.0-beahnap
6) zlib/1.2.13-gcc-12.2.0-qvwbld7
7) libxml2/2.10.3-gcc-12.2.0-6g4ulfn
8) ncurses/6.4-gcc-12.2.0-bt2tv43
9) hwloc/2.9.1-gcc-12.2.0-wjb3zv3
10) numactl/2.0.14-gcc-12.2.0-62dxa76
11) bzip2/1.0.8-gcc-12.2.0-yn6mmdj
12) pigz/2.7-gcc-12.2.0-5w24zpq
13) zstd/1.5.5-gcc-12.2.0-d3iesv2
14) tar/1.34-gcc-12.2.0-344crw2
15) gettext/0.21.1-gcc-12.2.0-htnecfu
16) openssl/3.1.1-gcc-12.2.0-xydqrfk
17) krb5/1.20.1-gcc-12.2.0-ywylqdh
18) libedit/3.1-20210216-gcc-12.2.0-uybrqun
19) libxcrypt/4.4.35-gcc-12.2.0-bnemwrw
20) openssh/9.3p1-gcc-12.2.0-nvgsowj
21) libevent/2.1.12-gcc-12.2.0-zgp5wia
22) pmix/4.2.3-gcc-12.2.0-ksjdukm
23) openmpi/4.1.5-gcc-12.2.0-ab5rikq
24) pkgconf/1.9.5-gcc-12.2.0-pdjoat6
25) hdf5/1.12.2-gcc-12.2.0-xwxzdqa
26) netcdf-c/4.7.4-gcc-12.2.0-5wzc2ic
27) asagi/1.0.1-gcc-12.2.0-xvz2l4l
28) gcc-runtime/12.2.0-gcc-12.2.0-v4wn2t2
29) impalajit/main-gcc-12.2.0-judjtis
30) nghttp2/1.52.0-gcc-12.2.0-x5wdgxs
31) curl/8.1.2-gcc-12.2.0-2s4wrx6
32) readline/8.2-gcc-12.2.0-ofdoevl
33) unzip/6.0-gcc-12.2.0-7wxq5cw
34) lua/5.3.2-gcc-12.2.0-zucnb2e
35) python/3.9.2-gcc-12.2.0-ikw34ao
36) yaml-cpp/0.6.2-gcc-12.2.0-adem7ot
37) easi/1.3.0-gcc-12.2.0-3egmupu
38) simmetrix-simmodsuite/17.0-220511-gcc-12.2.0-uzc6sef
39) metis/5.1.0-gcc-12.2.0-kcvzwx3
40) parmetis/4.0.3-gcc-12.2.0-minbyzl
41) zoltan/3.83-gcc-12.2.0-sl2xogx
42) pumi/2.2.7-gcc-12.2.0-jvajctp
43) pumgen/develop-gcc-12.2.0-dk4hwzp
44) intel-lm/1.0
45) tbb
46) compiler-rt
47) compiler
48) intel/2022
- Provide parameter/material files.
All the files required to reproduce the error is in the directory with the main script and subdirectory
PUMGEN_mesh.sh
/import/freenas-m-05-seissol/jwcwong/Tohoku/MESH
/import/freenas-m-05-seissol/jwcwong/Tohoku/MESH/Tohoku_v7_JIVSM_2404_vel_aware_0.5hz_1D
Screenshots/Console output
Mesh output (no refinement in the mesh)
Additional context
I have to load intel compiler and intel-lm math module to run pumgen. Would that be the case leading to the error?
Error encounter without module load intel intel-lm
pumgen: error while loading shared libraries: libimf.so:
Should it be equal to 2?
Line 77 in da94692
Segmentation Fault when Converting .neu File with PumGen
I encountered an issue while attempting to convert a .neu file generated with SimModeler v2024.0-240519 using PumGen. This (faults_250.zip) is the file i used for testing.
I compiled pumgen without simmetrix support using the following library versions:
The program crashes during the conversion process with the following error output:
(base) 017552119@cos-bmadden-dt:~/Faults/test_simple_500_0.15_8AR$ ./pumgen faults_250.neu test
Fri Jul 12 15:06:25, Info: No filtering enabled (contiguous storage)
Fri Jul 12 15:06:25, Info: Using 32-bit integer boundary type conditions, or 8 bit per face (i32).
Fri Jul 12 15:06:25, Info: Using Gambit mesh
Fri Jul 12 15:06:25, Warn: Gambit format does not seem to have a fixed boundary line length. Trying with variable line length
Fri Jul 12 15:06:25, Info: Read vertex coordinates
Fri Jul 12 15:06:25, Info: Reading vertices part 1 of 1
Fri Jul 12 15:06:26, Info: Read cell vertices
Fri Jul 12 15:06:26, Info: Reading elements part 1 of 1
Fri Jul 12 15:06:28, Info: Read cell groups
Fri Jul 12 15:06:28, Info: Reading group information part 1 of 1
Fri Jul 12 15:06:29, Info: Read boundary conditions
Fri Jul 12 15:06:29, Info: Reading boundary conditions part 1 of 1
[cos-bmadden-dt:1370791] *** Process received signal ***
[cos-bmadden-dt:1370791] Signal: Segmentation fault (11)
[cos-bmadden-dt:1370791] Signal code: Address not mapped (1)
[cos-bmadden-dt:1370791] Failing at address: 0x278
[cos-bmadden-dt:1370791] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f6e2dd11520]
[cos-bmadden-dt:1370791] [ 1] ./pumgen(+0x16375)[0x5562c0004375]
[cos-bmadden-dt:1370791] [ 2] ./pumgen(+0x16c15)[0x5562c0004c15]
[cos-bmadden-dt:1370791] [ 3] ./pumgen(+0x1904f)[0x5562c000704f]
[cos-bmadden-dt:1370791] [ 4] ./pumgen(+0x976f)[0x5562bfff776f]
[cos-bmadden-dt:1370791] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f6e2dcf8d90]
[cos-bmadden-dt:1370791] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f6e2dcf8e40]
[cos-bmadden-dt:1370791] [ 7] ./pumgen(+0xc025)[0x5562bfffa025]
[cos-bmadden-dt:1370791] *** End of error message ***
Segmentation fault (core dumped)
Upon running the program with gdb, I obtained the following backtrace:
Thread 1 "pumgen" received signal SIGSEGV, Segmentation fault.
0x000055555556a375 in int& std::vector<int, std::allocator<int> >::emplace_back<int>(int&&) ()
(gdb) backtrace
#0 0x000055555556a375 in int& std::vector<int, std::allocator<int> >::emplace_back<int>(int&&) ()
#1 0x000055555556ac15 in puml::ParallelGambitReader::readBoundaries(int*) ()
#2 0x000055555556d04f in SerialMeshFile<puml::ParallelGambitReader>::open(char const*) ()
#3 0x000055555555d76f in main ()
I also built a debug version instead of a release, and it seems to crash at a different location with a heap overflow
(base) 017552119@cos-bmadden-dt:~/Faults/test_simple_500_0.15_8AR$ ~/PUMGen/pumgen/debug-build/pumgen faults_250.neu test
Fri Jul 12 15:31:27, Info: No filtering enabled (contiguous storage)
Fri Jul 12 15:31:27, Info: Using 32-bit integer boundary type conditions, or 8 bit per face (i32).
Fri Jul 12 15:31:27, Info: Using Gambit mesh
Fri Jul 12 15:31:27, Warn: Gambit format does not seem to have a fixed boundary line length. Trying with variable line length
Fri Jul 12 15:31:27, Warn: Gambit format does not seem to have a fixed boundary line length. Trying with variable line length
Fri Jul 12 15:31:27, Warn: Gambit format does not seem to have a fixed boundary line length. Trying with variable line length
Fri Jul 12 15:31:27, Info: Read vertex coordinates
Fri Jul 12 15:31:27, Info: Reading vertices part 1 of 1
Fri Jul 12 15:31:29, Info: Read cell vertices
Fri Jul 12 15:31:29, Info: Reading elements part 1 of 1
Fri Jul 12 15:31:32, Info: Read cell groups
Fri Jul 12 15:31:32, Info: Reading group information part 1 of 1
=================================================================
==1374651==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x60400004f7b8 at pc 0x55ec870c54e2 bp 0x7ffd2eb949a0 sp 0x7ffd2eb94990
READ of size 8 at 0x60400004f7b8 thread T0
#0 0x55ec870c54e1 in puml::GambitReader::readGroups(unsigned long, unsigned long, puml::ElementGroup*) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x2c4e1)
#1 0x55ec870c77cd in puml::ParallelGambitReader::readGroups(int*) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x2e7cd)
#2 0x55ec870dee22 in SerialMeshFile<puml::ParallelGambitReader>::open(char const*) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x45e22)
#3 0x55ec870d3a76 in SerialMeshFile<puml::ParallelGambitReader>::SerialMeshFile(char const*, int, ompi_communicator_t*) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x3aa76)
#4 0x55ec870abbe9 in main /home/017552119/PUMGen/pumgen/src/pumgen.cpp:319
#5 0x7f9f391e9d8f in __libc_start_call_main ../sysdeps/nptl/libc_start_call_main.h:58
#6 0x7f9f391e9e3f in __libc_start_main_impl ../csu/libc-start.c:392
#7 0x55ec870a7bc4 in _start (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0xebc4)
0x60400004f7b8 is located 0 bytes to the right of 40-byte region [0x60400004f790,0x60400004f7b8)
allocated by thread T0 here:
#0 0x7f9f39fff1e7 in operator new(unsigned long) ../../../../src/libsanitizer/asan/asan_new_delete.cpp:99
#1 0x55ec870fb9ad in __gnu_cxx::new_allocator<puml::GambitReader::GroupSection>::allocate(unsigned long, void const*) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x629ad)
#2 0x55ec870f2eec in std::allocator_traits<std::allocator<puml::GambitReader::GroupSection> >::allocate(std::allocator<puml::GambitReader::GroupSection>&, unsigned long) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x59eec)
#3 0x55ec870e86f9 in std::_Vector_base<puml::GambitReader::GroupSection, std::allocator<puml::GambitReader::GroupSection> >::_M_allocate(unsigned long) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x4f6f9)
#4 0x55ec870da431 in std::vector<puml::GambitReader::GroupSection, std::allocator<puml::GambitReader::GroupSection> >::_M_default_append(unsigned long) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x41431)
#5 0x55ec870cec10 in std::vector<puml::GambitReader::GroupSection, std::allocator<puml::GambitReader::GroupSection> >::resize(unsigned long) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x35c10)
#6 0x55ec870c1a15 in puml::GambitReader::open(char const*) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x28a15)
#7 0x55ec870dc404 in ParallelMeshReader<puml::GambitReader>::open(char const*) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x43404)
#8 0x55ec870de9a6 in SerialMeshFile<puml::ParallelGambitReader>::open(char const*) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x459a6)
#9 0x55ec870d3a76 in SerialMeshFile<puml::ParallelGambitReader>::SerialMeshFile(char const*, int, ompi_communicator_t*) (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x3aa76)
#10 0x55ec870abbe9 in main /home/017552119/PUMGen/pumgen/src/pumgen.cpp:319
#11 0x7f9f391e9d8f in __libc_start_call_main ../sysdeps/nptl/libc_start_call_main.h:58
SUMMARY: AddressSanitizer: heap-buffer-overflow (/home/017552119/PUMGen/pumgen/debug-build/pumgen+0x2c4e1) in puml::GambitReader::readGroups(unsigned long, unsigned long, puml::ElementGroup*)
Shadow bytes around the buggy address:
0x0c0880001ea0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
0x0c0880001eb0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
0x0c0880001ec0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
0x0c0880001ed0: fa fa 00 00 00 00 00 00 fa fa fd fd fd fd fd fd
0x0c0880001ee0: fa fa fd fd fd fd fd fd fa fa fd fd fd fd fd fd
=>0x0c0880001ef0: fa fa 00 00 00 00 00[fa]fa fa fd fd fd fd fd fd
0x0c0880001f00: fa fa fd fd fd fd fd fd fa fa fa fa fa fa fa fa
0x0c0880001f10: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
0x0c0880001f20: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
0x0c0880001f30: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
0x0c0880001f40: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
Shadow byte legend (one shadow byte represents 8 application bytes):
Addressable: 00
Partially addressable: 01 02 03 04 05 06 07
Heap left redzone: fa
Freed heap region: fd
Stack left redzone: f1
Stack mid redzone: f2
Stack right redzone: f3
Stack after return: f5
Stack use after scope: f8
Global redzone: f9
Global init order: f6
Poisoned by user: f7
Container overflow: fc
Array cookie: ac
Intra object redzone: bb
ASan internal: fe
Left alloca redzone: ca
Right alloca redzone: cb
Shadow gap: cc
==1374651==ABORTING
Has anyone else encountered a similar error? If so, do you have any suggestions or ideas on what I could try to resolve this issue?
pumgen crashes if properties given by a LayeredModel (VelocityAwareMeshing)
I've noticed that VelocityAwareMeshing seems to always crash with the velocity is given by a LayeredModel.
Here is an extract of the log:
Wed Feb 22 14:42:28, Info: face id: 116 , MSize = 1000
Wed Feb 22 14:42:28, Info: face id: 120 , MSize = 1000
Wed Feb 22 14:42:28, Info: face id: 122 , MSize = 1000
Wed Feb 22 14:42:28, Info: Enabling velocity aware meshing
Wed Feb 22 14:42:28, Info: Gradation rate = 0.8
Wed Feb 22 14:42:28, Info: Target equivolume AspectRatio = 12
Wed Feb 22 14:42:28, Info: Target equiarea AspectRatio = 6
Wed Feb 22 14:42:28, Info: Starting the surface mesher
Wed Feb 22 14:42:28, Info: Progress: Surface Meshing
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 8 with PID 0 on node exception exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
Here is the xml file:
<freeSurface>119</freeSurface>
<!-- hypocenter-->
<boundaryCondition tag="65">121</boundaryCondition>
<!-- fault 7.8-->
<boundaryCondition tag="66">101,107,112,114,121</boundaryCondition>
<!-- fault 7.5-->
<boundaryCondition tag="67">97,109,115,116,120,122</boundaryCondition>
<!-- extras fault 7.8 -->
<boundaryCondition tag="68">110,105</boundaryCondition>
<absorbing>93,95,103,104,108</absorbing>
<surfaceMSize value="1000">101,107,112,114,121,110,105</surfaceMSize>
<surfaceMSize value="1000">97,109,115,116,120,122</surfaceMSize>
<area_AspectRatio value="6"/>
<vol_AspectRatio value="12"/>
<SurfaceMeshing SmoothingLevel="1" SmoothingType="Gradient" DiscreteAngle="15.0" Snap="0"></SurfaceMeshing>
<VolumeMeshing SmoothingLevel="1" SmoothingType="Gradient" SetOptimisation="1"></VolumeMeshing>
<gradation value="0.8"/>
<globalMSize value="20e3"/>
<VelocityAwareMeshing easiFile="Mw_78_Turkey_rhomulambda1D_Guvercin_et_al.yaml" elementsPerWaveLength="3">
<VelocityRefinementCuboid frequency="0.1" centerX="0" centerY="0" centerZ="-15e3"
halfSizeX="40e10" halfSizeY="15e10" halfSizeZ="15e10" bypassFindRegionAndUseGroup="1"/>
</VelocityAwareMeshing>
and here is the yaml file:
!LayeredModel
map: !AffineMap
matrix:
z1: [0.0, 0.0, 1.0]
translation:
z1: 0
interpolation: lower
parameters: [rho, mu, lambda, plastCo]
nodes:
-1000.0: [2464.9689710139387, 14555395276.94021, 21249511511.522747, 5822158.1107760845]
-1000000.0: [3400.203751580001, 72261470148.95335, 89717096148.43964, 28904588.059581343]
if I use a LuaMap instead:
!LuaMap
returns: [rho, mu, lambda]
function: |
function f (x)
if (x["z"] >= -1000.0) then
rho = 2464.9689710139387
mu = 14555395276.94021
lambda = 21249511511.522747
elseif (x["z"] >= -1000000.0) then
rho = 3400.203751580001
mu = 72261470148.95335
lambda = 89717096148.43964
end
return {
rho = rho,
mu = mu,
lambda = lambda
}
end
I'm able to generate the mesh.
the setup is available on exception, at /export/dump/ulrich/PUMGEN_folder/bug_layered_model
gmsh2.2 mesh generated on windows cannot be converted
Hi,
I'm collaborating with a windows user and he generated a mesh with gmsh 4.9.? for me.
The mesh cannot be converted with pumgen, which gets stuck.
When generating the mesh on linux, the mesh can easily be converted.
Attached are the geo file and the 2 msh files (we changed the mesh sizes to have a lower cell count).
(base) ulrich@exception:/export/dump/ulrich$ pumgen -s msh2 ExtendedBottom_SeisSol-small_ubuntu.msh
Wed Mar 15 14:46:49, Info: Using GMSH mesh format 2 (msh2) mesh
Wed Mar 15 14:46:49, Info: Create APF connectivity
Wed Mar 15 14:46:49, Info: Set coordinates in APF
Wed Mar 15 14:46:49, Info: Mesh size: 22913
Wed Mar 15 14:46:49, Info: Minimum insphere found: 0.529276
Wed Mar 15 14:46:49, Info: Writing cells
Wed Mar 15 14:46:49, Info: Writing vertices
Wed Mar 15 14:46:49, Info: Writing group information
Wed Mar 15 14:46:49, Info: Writing boundary condition
Wed Mar 15 14:46:49, Info: Writing XDMF file
Wed Mar 15 14:46:49, Info: Finished successfully
(base) ulrich@exception:/export/dump/ulrich$ pumgen -s msh2 ExtendedBottom_SeisSol-small_windows.msh
Wed Mar 15 14:46:57, Info: Using GMSH mesh format 2 (msh2) mesh
additional dependencies have been found in case of compilation with intel compiler
Hi all,
So, I was installing PUMGen on my local machine using intel compiler. I found there were similar issues before, for example (from Thomas):
...
H5.c:(.text+0xcb): undefined reference to __intel_sse2_strlen' H5.c:(.text+0x11c): undefined reference to __intel_sse2_strlen'
H5.c:(.text+0x190): undefined reference to __intel_sse2_strlen' H5.c:(.text+0x1e1): undefined reference to __intel_sse2_strlen'
H5.c:(.text+0x27c): undefined reference to `__intel_sse2_strlen'
...
So, I found where the problem was in my case. Basically, a declaration of two libs was missed in SConscript file, namely: irc, svml. Maybe gcc compiler is able to find these libs for itself using the standard lookup paths but intel cannot. I added two lines two SConstruct file:
env.Append(LIBPATH=['<path to my intel installation>/compilers_and_libraries/linux/lib/intel64/'])
env.Append(LIBS=['irc', 'svml']), and I managed to compile PUMGen after that. Basically, hdf5 is looking for these two libs
Compiling with MPI 4
Compiling with the command on my local machine (Ubuntu 20.04)
cmake .. \
> -DCMAKE_C_COMPILER="`which mpicc`" \
> -DCMAKE_CXX_COMPILER="`which mpiCC`" \
> -DCMAKE_C_FLAGS="-O2 -g -Wall" \
> -DCMAKE_CXX_FLAGS="-O2 -g -Wall" \
> -DCMAKE_INSTALL_PREFIX=/usr/local
resulsts with the error:
In file included from /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277,
from /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2868,
from /home/primrose/Installed/core/pcu/PCU.h:16,
from /home/primrose/Installed/core/apf/apfMesh.cc:8:
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function ‘virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)’:
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: error: cast between incompatible function types from ‘void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Werror=cast-function-type]
121 | (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:123:59: error: cast between incompatible function types from ‘void (*)(const void*, void*, int, const MPI::Datatype&)’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Werror=cast-function-type]
123 | ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func);
| ^~~~
...
Could it be that it does not support MPI 4 but only 3?
primrose@primrose:~/Installed/core/build$ mpiexec --version
mpiexec (OpenRTE) 4.0.3
Boundary conditions not detected since new pull request?
I was trying to generate a small Sumatra mesh for debugging purpose.
Below the xml and the log file from pumgen/xml branch.
<freeSurface>25,26,27,29</freeSurface>
<absorbing>18,30</absorbing>
<dynamicRupture>19,20,21,23,24,31,32</dynamicRupture>
<comment text='19,20: forethrust 31,32:Northern BT 23,24: Southern BT 21: Subduction interface'/>
<globalMSize value="100e3"/>
<surfaceMSize value="3000.0">19,20,21,23,24,31,32</surfaceMSize>
<area_AspectRatio value="6"/>
<vol_AspectRatio value="12"/>
<SurfaceMeshing SmoothingLevel="1" SmoothingType="Gradient" DiscreteAngle="15.0" Snap="0"></SurfaceMeshing>
<VolumeMeshing SmoothingLevel="1" SmoothingType="Gradient" SetOptimisation="1"></VolumeMeshing>
<gradation value="2.0"/>
/var/spool/slurm/job728337/slurm_script: line 43: ulimit: core file size: cannot modify limit: Operation not permitted
Fri Jul 03 10:31:56, Info: Using SimModSuite
Fri Jul 03 10:31:56, Info: Loading model
Fri Jul 03 10:32:10, Info: Extracting cases
Fri Jul 03 10:32:10, Info: surface smoothing option: surfaceSmoothingLevel surfaceSmoothingType surfaceFaceRotationLimit Snap 1 1 15 0
Fri Jul 03 10:32:10, Info: volume smoothing option: volumeSmoothingLevel volumrSmoothingType 1 1
Fri Jul 03 10:32:10, Info: Setting cases
Fri Jul 03 10:32:10, Info: globalMSize = 100000
Fri Jul 03 10:32:10, Info: faceid: 19 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info: faceid: 20 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info: faceid: 21 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info: faceid: 23 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info: faceid: 24 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info: faceid: 31 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info: faceid: 32 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info: Gradation rate = 2
Fri Jul 03 10:32:10, Info: Target equivolume AspectRatio = 12
Fri Jul 03 10:32:10, Info: Target equiarea AspectRatio = 6
Fri Jul 03 10:32:10, Info: Starting the surface mesher
The following kind of lines are missing:
Tue Mar 24 10:24:24, Info: faceBound[ 25 ] = 1
mesh > 32e6 generated with pumgen@master or pumgen@bypass-apf failed when read by seissol
dss/dsshome1/0F/ra75qeh2/seisNonl/SeisSol/submodules/PUML/PUML.h:1010: unsigned int PUML::PUML<Topo>::addFace(unsigned int, unsigned int) [with PUML::TopoType Topo = PUML::TETRAHEDRON]: Assertion `m_faces[lid].m_upward[1] == -1' failed.
Ziua, Nicolas, please give details.
Compilation error with GMSH support
Describe the issue:
Compiling pumgen (current master:498ab01) with
set(CMAKE_CXX_STANDARD 17) in CMakeLists.txt give CMake error:
Target "cmTC_9516a" requires the language dialect "CXX17" , but CMake does not know the compile flags to use to enable it.
then I tried changing CMakeLists.txt to set(CMAKE_CXX_STANDARD 11) removed previous CMake error and lead to another error:
PUMGen/src/third_party/GMSHLexer.h(49): error: "auto" function requires a trailing return type
auto getIdentifier() const { return identifier; }
PUMGen/src/third_party/GMSHLexer.h(50): error: "auto" function requires a trailing return type
auto getInteger() const { return integer; }
PUMGen/src/third_party/GMSHLexer.h(51): error: "auto" function requires a trailing return type
auto getReal() const { return real; }
PUMGen/src/third_party/GMSHLexer.h(52): error: "auto" function requires a trailing return type
auto getSourceLoc() const { return loc; }
PUMGen/src/third_party/GMSHParser.h(8): catastrophic error: cannot open source file "optional"
#include
I tried to exclude all related to GMSH from
a) on CMakeLists.txt:
${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/ParallelGMSHReader.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/third_party/GMSHLexer.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/third_party/GMSHParser.cpp
b) on src/pumgen.cpp:
#include "meshreader/ParallelGMSHReader.h"
remove "msh2":
const char* source[] = {"gambit", "fidap", "msh2", "netcdf", "apf", "simmodsuite"};
and remove "case 2" and modify other case numbers according number in case list:
case 2: logInfo(rank) << "Using GMSH mesh format 2 (msh2) mesh"; meshInput = new SerialMeshFile<puml::ParallelGMSHReader>(inputFile); break;
with this, pumgen compiled successfully.
To Reproduce:
intel/2017
mpi.intel/2017
cmake/3.10.3
cmake .. -DCMAKE_PREFIX_PATH=$pumiDir -DSIMMETRIX=ON
-DSIMMETRIX_ROOT=$simmetrixDir -DCMAKE_BUILD_TYPE=Release
-DCMAKE_C_COMPILER=mpiicc \
-DCMAKE_CXX_COMPILER=mpiicpc
make -j 4
SIM_PARTITINED_WRAPPER_LIB
Should not default to mpich3
Cf. SIM_LIB in scorec
pumgen mesh64 fails converting small mesh
pumgen master:
(base) ulrich@exception:/export/dump/ulrich/PUMGEN_folder/GAB$ pumgen -s msh2 ExtendedBottom_1703_small_no_LD_seissol.msh
Tue Oct 10 14:33:48, Info: Using GMSH mesh format 2 (msh2) mesh
Tue Oct 10 14:33:48, Info: Create APF connectivity
Tue Oct 10 14:33:49, Info: Set coordinates in APF
Tue Oct 10 14:33:49, Info: Mesh size: 140019
Tue Oct 10 14:33:49, Info: Minimum insphere found: 0.110456
Tue Oct 10 14:33:49, Info: Writing cells
Tue Oct 10 14:33:49, Info: Writing vertices
Tue Oct 10 14:33:49, Info: Writing group information
Tue Oct 10 14:33:49, Info: Writing boundary condition
Tue Oct 10 14:33:49, Info: Writing XDMF file
Tue Oct 10 14:33:49, Info: Finished successfully
pumgen mesh64:
Tue Oct 10 14:34:26, Info: No filtering enabled (contiguous storage)
Tue Oct 10 14:34:26, Info: Using GMSH mesh format 2 (msh2) mesh
Tue Oct 10 14:34:27, Info: Create APF connectivity
Tue Oct 10 14:34:27, Info: Set coordinates in APF
[exception:1331639] *** Process received signal ***
[exception:1331639] Signal: Segmentation fault (11)
[exception:1331639] Signal code: Address not mapped (1)
[exception:1331639] Failing at address: 0x10
[exception:1331639] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x13140)[0x14ddacdc6140]
[exception:1331639] [ 1] pumgen[0xe93246]
[exception:1331639] [ 2] pumgen[0xe936ea]
[exception:1331639] [ 3] pumgen[0xe938e9]
[exception:1331639] [ 4] pumgen[0xe426fc]
[exception:1331639] [ 5] pumgen[0xe42bd8]
[exception:1331639] [ 6] pumgen[0xb83b74]
[exception:1331639] [ 7] pumgen[0x41d81d]
[exception:1331639] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xea)[0x14ddab8e8d0a]
[exception:1331639] [ 9] pumgen[0x42105a]
[exception:1331639] *** End of error message ***
Segmentation fault
Pumgen smooth specific faces
The current pumgen mesh attributes xml has an option of
<SurfaceMeshing SmoothingLevel="3" SmoothingType="Gradient" DiscreteAngle="1.0" Snap="0"/>
Would it be able to specify faces to smooth instead of smoothing all the surfaces in the mesh?
It would be useful to create the complex geometry in most of the subduction zone.
Compiling PUMGen with spack in Shaheen II
Describe the issue.
I tried compiling PUMGen with spack with simmetrix on Shaheen II and results in the following error.
The process followed is from here https://github.com/SeisSol/PUMGen/wiki/How-to-compile-PUMGen
It works fine without simmetrix support.
Warning: Missing a source id for pumgen@develop
==> [email protected] : has external module in ['cmake/3.22.1']
[+] /sw/xc40cle7up03/cmake/3.22.1/sles15gcc7.5.0 (external cmake-3.22.1-qjzmxoytejx2kwaimenr4ujer6vt4pvk)
==> [email protected] : has external module in ['cray-mpich/7.7.20']
[+] /opt/cray/pe/mpt/7.7.20/gni/mpich-gnu/8.2 (external mpich-7.7.20-bp2ketiytzqupkh6d2fxcrmq4yjmvrmy)
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/pkgconf-1.8.0-dmhzeibcqxi6yg4exzxag33jfqujas4u
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/zlib-1.2.12-2iy6zo4llskya72xxnv4r52nko77n5yr
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/libsigsegv-2.13-7nszos2mb27ryu723ecv6qywsmleytbn
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/berkeley-db-18.1.40-f6yqlyfh7wjo5z6w4qqjmmtd7cczhjcz
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/libiconv-1.16-7kytbtbz2kbbhrqgk4op6n3p4pc65ydi
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/unzip-6.0-5rypjotvucn7ybwg4rg2i53nsx53audx
[+] /project/k1589/aquibt/myLibs/meshing_software/simmodeler/17.0-230211/ (external MeshSimAdvanced-17.0-230211-rqnbybfe2gixxb24a7iljmbxv2pks3ck)
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/metis-5.1.0-bg7sv5uhluisethpqx4ucwmdhdyc6374
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/yaml-cpp-0.6.2-pfuf254e5xskpx633r5yfrv7vdzzdsdq
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/ncurses-6.2-ogfyosttxxa2nnd5bhe2gz6eqbypyclw
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/hdf5-1.12.2-aeb4we5wlzg6eihfbs7qnccorsjjf5yp
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/m4-1.4.19-elt3djcwlagzqn7hh7fy5sxwu66yiclc
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/diffutils-3.8-vzww3xpckh42iwf7pj6ajo5xrb4srit2
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/parmetis-4.0.3-gnfpqd6nkjjg4am2rxzlb2iolrun2ufc
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/readline-8.1-ny5b7atuia442wolp6bsjk3fj4hhl73w
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/libtool-2.4.7-kh54yxuwrtgpgzgh47qnwvctwkqtxuwp
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/netcdf-c-4.7.4-jh5i74zk7ddgb56axyivuwzpxyzxxw2g
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/bzip2-1.0.8-ebhtdwpuvbsgxmmtugns5aydyzi67bp7
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/gdbm-1.19-2imglgcvgz5avog5nkzfs7r6vh4sjbjc
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/perl-5.34.1-oy5gobc3rknssbkfgqk7qcoglsznf2sj
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/autoconf-2.69-s5tnyypge46n3dzdug3ld6loq6ifuvg3
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/openssl-1.1.1o-3epcw2my3ryqvnqraxjfzsgz2zv5hebn
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/automake-1.16.5-hmdsbthd6hupeae5oyw5x7o3yo3wtmp6
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/curl-7.83.0-y6rehiyz46rug2hznic6kg54n2qndpk7
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/numactl-2.0.14-sadzwhwiktstycpaauiznlenepqs2f7s
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/zoltan-3.83-pdznfhwg7f4vopqjyhblwetjmovwmz3r
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/lua-5.3.2-jbld6b5jyg7rrteuaobsxayf7bipg4yd
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/asagi-1.0.1-4y25gc35plzxmiguxh44zhcunjatmezj
==> Installing pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw
==> No binary for pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw found: installing from source
==> Using cached archive: /lustre2/project/k1589/aquibt/myLibs/spack/var/spack/cache/_source-cache/git//SCOREC/core.git/a295720d7b4828282484f2b78bac1f6504512de4.tar.gz
==> Warning: Fetching from mirror without a checksum!
This package is normally checked out from a version control system, but it has been archived on a spack mirror. This means we cannot know a checksum for the tarball in advance. Be sure that your connection to this mirror is secure!
==> No patches needed for pumi
==> pumi: Executing phase: 'cmake'
==> Error: ProcessError: Command exited with status 1:
'cmake' '-G' 'Unix Makefiles' '-DCMAKE_INSTALL_PREFIX:STRING=/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw' '-DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo' '-DBUILD_TESTING:BOOL=OFF' '-DCMAKE_INTERPROCEDURAL_OPTIMIZATION:BOOL=OFF' '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON' '-DCMAKE_INSTALL_RPATH:STRING=/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw/lib;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw/lib64;/opt/cray/pe/mpt/7.7.20/gni/mpich-gnu/8.2/lib;/project/k1589/aquibt/myLibs/meshing_software/simmodeler/17.0-230211/lib;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/zoltan-3.83-pdznfhwg7f4vopqjyhblwetjmovwmz3r/lib;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/metis-5.1.0-bg7sv5uhluisethpqx4ucwmdhdyc6374/lib;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/parmetis-4.0.3-gnfpqd6nkjjg4am2rxzlb2iolrun2ufc/lib;/opt/gcc/11.2.0/snos' '-DCMAKE_PREFIX_PATH:STRING=/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/zoltan-3.83-pdznfhwg7f4vopqjyhblwetjmovwmz3r;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/parmetis-4.0.3-gnfpqd6nkjjg4am2rxzlb2iolrun2ufc;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/metis-5.1.0-bg7sv5uhluisethpqx4ucwmdhdyc6374;/project/k1589/aquibt/myLibs/meshing_software/simmodeler/17.0-230211/;/opt/cray/pe/mpt/7.7.20/gni/mpich-gnu/8.2;/sw/xc40cle7up03/cmake/3.22.1/sles15gcc7.5.0' '-DSCOREC_CXX_WARNINGS=OFF' '-DENABLE_ZOLTAN:BOOL=ON' '-DCMAKE_C_COMPILER=/lustre2/project/k1589/aquibt/myLibs/spack/lib/spack/env/gcc/gcc' '-DCMAKE_CXX_COMPILER=/lustre2/project/k1589/aquibt/myLibs/spack/lib/spack/env/gcc/g++' '-DBUILD_SHARED_LIBS:BOOL=OFF' '-DCMAKE_Fortran_COMPILER=/lustre2/project/k1589/aquibt/myLibs/spack/lib/spack/env/gcc/gfortran' '-DPUMI_FORTRAN_INTERFACE:BOOL=OFF' '-DMDS_ID_TYPE=long' '-DSKIP_SIMMETRIX_VERSION_CHECK=ON' '-DIS_TESTING:BOOL=OFF' '-DMESHES=/tmp/aquibt/spack-stage/spack-stage-pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw/spack-src/pumi-meshes' '-DENABLE_SIMMETRIX=ON' '-DSIM_DISCRETE=ON' '-DSIM_MPI=mpich7' '/tmp/aquibt/spack-stage/spack-stage-pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw/spack-src'
1 error found in build log:
37 -- ENABLE_SIMMETRIX: ON
38 -- ENABLE_OMEGA_H: OFF
39 -- ENABLE_FPP: OFF
40 -- Skipping Simmetrix SimModSuite version check. This may result in undefined behavior
41 -- Building with SimModSuite 17.0.230211
42 -- SIM_ARCHOS x64_rhel7_gcc48
>> 43 CMake Error at cmake/FindSimModSuite.cmake:33 (message):
44 simmetrix library SimPartitionWrapper-mpich7 not found in
45 Call Stack (most recent call first):
46 cmake/FindSimModSuite.cmake:167 (simLibCheck)
47 CMakeLists.txt:114 (find_package)
48
49
See build log for details:
/tmp/aquibt/spack-stage/spack-stage-pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw/spack-build-out.txt
To reproduce
-
Simmodeler (17.0-230211) installed from http://www.simmetrix.com/index.php/support/support-downloads/download-release?prod=M&release=17.0-230211
-
All zip files are combined using
for filename in *.tgz
do
tar zxf $filename
done
- Loaded modules on Shaheeen II
1) modules/3.2.11.4 16) pmi/5.0.17
2) craype-network-aries 17) dmapp/7.1.1-7.0.3.1_3.49__g93a7e9f.ari
3) cray-mpich/7.7.18 18) gni-headers/5.0.12.0-7.0.3.1_3.32__gd0d73fe.ari
4) slurm/slurm 19) xpmem/2.2.27-7.0.3.1_3.31__gada73ac.ari
5) dws/3.0.36-7.0.3.1_3.55__g6985c90.ari 20) job/2.2.4-7.0.3.1_3.40__g36b56f4.ari
6) eproxy/2.0.24-7.0.3.1_3.25__g8e04b33.ari 21) dvs/2.12_2.2.224-7.0.3.1_3.50__gc77db2af
7) craype-haswell 22) alps/6.6.67-7.0.3.1_3.48__gb91cd181.ari
8) xalt/1.1.2 23) rca/2.2.20-7.0.3.1_3.53__g8e3fb5b.ari
9) darshan/3.3.1 24) atp/3.14.5
10) ksl/ksl 25) perftools-base/21.09.0
11) gcc/11.2.0 26) PrgEnv-gnu/6.0.10
12) craype/2.7.10 27) python/3.10.1-cdl
13) cray-libsci/20.09.1 28) cmake/3.26.4
14) udreg/2.3.2-7.0.3.1_3.50__g5f0d670.ari 29) seissol-env-develop-gcc-11.2.0-q7rdeu3
15) ugni/6.0.14.0-7.0.3.1_6.31__g8101a58.ari
- Edited /.spack/packages.yaml file
packages:
simmetrix-simmodsuite:
externals:
- spec: [email protected]
prefix: /project/k1589/aquibt/myLibs/meshing_software/simmodeler/17.0-230211/
I do not see any [email protected] file in simmodeler directory.
Compiling core on heisenbug
Hi,
I know it is not directly related to PUMGen, but before possibly opening an issue on core, I wanted to get some feedback.
I'm having trouble compiling core on heisenbug (LMU cluster).
module loaded
Currently Loaded Modulefiles:
1) paraview/5.10.0(default) 2) gcc/10.2.0(default) 3) mpi.ompi/4.1.0(default)
Environment variables:
VERSION="SeisSol-GPU-build"
BASE=/export/dump/ulrich
export SEISSOL_INSTALL_DIR=$BASE/${VERSION}/
export CC=`which mpicc`
#export MPICC=`which mpicc`
export CXX=`which mpiCC`
#export MPICXX=`which mpiCC`
export FC=`which mpif90`
export PATH=$SEISSOL_INSTALL_DIR/bin:$PATH
export LIBRARY_PATH=$SEISSOL_INSTALL_DIR/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=$SEISSOL_INSTALL_DIR/lib:$LD_LIBRARY_PATH
export PKG_CONFIG_PATH=$SEISSOL_INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH
export CMAKE_PREFIX_PATH=$SEISSOL_INSTALL_DIR:$CMAKE_PREFIX_PATH
export CPATH=$SEISSOL_INSTALL_DIR/include:$CPATH
export CPLUS_INCLUDE_PATH=$SEISSOL_INSTALL_DIR/include:$CPLUS_INCLUDE_PATH
export C_INCLUDE_PATH=$SEISSOL_INSTALL_DIR/include:$C_INCLUDE_PATH
export myLibs=/export/dump/ulrich/myLibs/
export path_to_SimModeler=$myLibs/simModelerLib/16.0-220326/
export mpi_name=mpich3
export path_to_pumi=$myLibs/core/
export path_to_SimModeler_lib=$path_to_SimModeler/lib/x64_rhel8_gcc83
export path_to_SimModeler_include_dir=$path_to_SimModeler/include
export path_to_hdf5=/export/dump/ulrich/SeisSol-GPU-build/
compilations process and error:
ulrich@heisenbug:/export/dump/ulrich/myLibs/core$ mkdir build && cd build
ulrich@heisenbug:/export/dump/ulrich/myLibs/core/build$ cmake .. \
> -DCMAKE_C_COMPILER="`which mpicc`" \
> -DCMAKE_CXX_COMPILER="`which mpiCC`" \
> -DSCOREC_EXTRA_C_FLAGS="-O2 -g -Wall" \
> -DSCOREC_EXTRA_CXX_FLAGS="-O2 -g -Wall" \
> -DCMAKE_INSTALL_PREFIX=$path_to_pumi \
> -DENABLE_SIMMETRIX=ON \
> -DSIM_MPI=$mpi_name \
> -DSIMMETRIX_LIB_DIR=$path_to_SimModeler_lib \
> -DSIMMODSUITE_INCLUDE_DIR=$path_to_SimModeler_include_dir
-- The CXX compiler identification is GNU 10.2.0
-- The C compiler identification is GNU 10.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/software/openmpi/buster/4.1.0_gcc-10.2.0/bin/mpiCC - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/software/openmpi/buster/4.1.0_gcc-10.2.0/bin/mpicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- CMAKE_VERSION: 3.18.4
-- SCOREC_VERSION: 2.2.7
-- BUILD_TESTING: OFF
-- CMAKE_INSTALL_PREFIX: /export/dump/ulrich/myLibs/core
-- BUILD_SHARED_LIBS: OFF
-- CMAKE_CXX_FLAGS: -O2 -g -Werror -Wall -Wextra -Wno-strict-overflow -O2 -g -Wall
-- CMAKE_CXX_FLAGS = -O2 -g -Werror -Wall -Wextra -Wno-strict-overflow -O2 -g -Wall
-- Try C99 C flag = [ ]
-- Performing Test C99_FLAG_DETECTED
-- Performing Test C99_FLAG_DETECTED - Success
-- CMAKE_C_FLAGS = -O2 -g -Werror -Wall -Wextra -Wno-strict-overflow -O2 -g -Wall
-- IS_TESTING: OFF
-- MESHES: /export/dump/ulrich/myLibs/core/pumi-meshes
-- BUILD_EXES: ON
-- PUMI_FORTRAN_INTERFACE: OFF
-- PUMI_PYTHON_INTERFACE: OFF
-- MPIRUN: /opt/software/openmpi/buster/4.1.0_gcc-10.2.0/bin/mpirun -np
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.13") found components: doxygen dot
-- ENABLE_SIMMETRIX: ON
-- ENABLE_OMEGA_H: OFF
-- ENABLE_FPP: OFF
-- Building with SimModSuite 16.0.220326
-- SIM_ARCHOS x64_rhel8_gcc83
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
CMake Warning (dev) at /usr/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:273 (message):
The package name passed to `find_package_handle_standard_args`
(SIMMODSUITE) does not match the name of the calling package (SimModSuite).
This can lead to problems in calling code that expects `find_package`
result variables (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
cmake/FindSimModSuite.cmake:177 (find_package_handle_standard_args)
CMakeLists.txt:114 (find_package)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found SIMMODSUITE: /export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimPartitionedMesh-mpi.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimDiscrete.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimField.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimAdvMeshing.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimPartitionedMesh-mpi.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimMeshing.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimMeshTools.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimModel.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimPartitionWrapper-mpich3.a
-- LION_COMPRESS: OFF
-- PCU_COMPRESS: OFF
-- ENABLE_FIELDSIM: OFF
-- MDS_SET_MAX: 256
-- MDS_ID_TYPE: int
-- ENABLE_ZOLTAN: OFF
-- Looking for clock_gettime
-- Looking for clock_gettime - found
-- ENABLE_STK: OFF
-- ENABLE_STK_MESH: OFF
-- ENABLE_DSP: OFF
-- Looking for mallinfo2
-- Looking for mallinfo2 - not found
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
SCOREC_EXTRA_C_FLAGS
-- Build files have been written to: /export/dump/ulrich/myLibs/core/build
ulrich@heisenbug:/export/dump/ulrich/myLibs/core/build$ make
Scanning dependencies of target lion
[ 1%] Building CXX object lion/CMakeFiles/lion.dir/lionBase64.cc.o
[ 1%] Building C object lion/CMakeFiles/lion.dir/lionPrint.c.o
[ 1%] Building CXX object lion/CMakeFiles/lion.dir/lionNoZLib.cc.o
[ 1%] Linking CXX static library liblion.a
[ 1%] Built target lion
Scanning dependencies of target pcu
[ 1%] Building C object pcu/CMakeFiles/pcu.dir/pcu.c.o
[ 1%] Building C object pcu/CMakeFiles/pcu.dir/pcu_aa.c.o
[ 2%] Building C object pcu/CMakeFiles/pcu.dir/pcu_coll.c.o
[ 2%] Building C object pcu/CMakeFiles/pcu.dir/pcu_io.c.o
[ 2%] Building C object pcu/CMakeFiles/pcu.dir/pcu_buffer.c.o
[ 2%] Building C object pcu/CMakeFiles/pcu.dir/pcu_mpi.c.o
[ 2%] Building C object pcu/CMakeFiles/pcu.dir/pcu_msg.c.o
[ 4%] Building C object pcu/CMakeFiles/pcu.dir/pcu_order.c.o
[ 4%] Building C object pcu/CMakeFiles/pcu.dir/pcu_pmpi.c.o
[ 4%] Building C object pcu/CMakeFiles/pcu.dir/pcu_util.c.o
[ 4%] Building C object pcu/CMakeFiles/pcu.dir/noto/noto_malloc.c.o
[ 4%] Building C object pcu/CMakeFiles/pcu.dir/reel/reel.c.o
[ 4%] Linking C static library libpcu.a
[ 4%] Built target pcu
Scanning dependencies of target gmi
[ 4%] Building C object gmi/CMakeFiles/gmi.dir/gmi.c.o
[ 4%] Building C object gmi/CMakeFiles/gmi.dir/agm.c.o
[ 4%] Building C object gmi/CMakeFiles/gmi.dir/gmi_base.c.o
[ 4%] Building C object gmi/CMakeFiles/gmi.dir/gmi_file.c.o
[ 5%] Building C object gmi/CMakeFiles/gmi.dir/gmi_lookup.c.o
[ 5%] Building C object gmi/CMakeFiles/gmi.dir/gmi_mesh.c.o
[ 5%] Building C object gmi/CMakeFiles/gmi.dir/gmi_null.c.o
[ 5%] Building C object gmi/CMakeFiles/gmi.dir/gmi_analytic.c.o
[ 5%] Linking CXX static library libgmi.a
[ 5%] Built target gmi
Scanning dependencies of target gmi_sim
[ 6%] Building CXX object gmi_sim/CMakeFiles/gmi_sim.dir/gmi_sim.cc.o
In file included from /opt/software/openmpi/buster/4.1.0_gcc-10.2.0/include/openmpi/ompi/mpi/cxx/mpicxx.h:277,
from /opt/software/openmpi/buster/4.1.0_gcc-10.2.0/include/mpi.h:2887,
from /export/dump/ulrich/myLibs/core/pcu/PCU.h:16,
from /export/dump/ulrich/myLibs/core/gmi_sim/gmi_sim.cc:10:
/opt/software/openmpi/buster/4.1.0_gcc-10.2.0/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function ‘virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)’:
/opt/software/openmpi/buster/4.1.0_gcc-10.2.0/include/openmpi/ompi/mpi/cxx/op_inln.h:121:25: error: cast between incompatible function types from ‘void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Werror=cast-function-type]
121 | (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/software/openmpi/buster/4.1.0_gcc-10.2.0/include/openmpi/ompi/mpi/cxx/op_inln.h:123:38: error: cast between incompatible function types from ‘void (*)(const void*, void*, int, const MPI::Datatype&)’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Werror=cast-function-type]
123 | ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
cc1plus: all warnings being treated as errors
make[2]: *** [gmi_sim/CMakeFiles/gmi_sim.dir/build.make:82: gmi_sim/CMakeFiles/gmi_sim.dir/gmi_sim.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:876: gmi_sim/CMakeFiles/gmi_sim.dir/all] Error 2
make: *** [Makefile:160: all] Error 2
Any idea?
pumgen was not compiling because of hdf5
We tried installing pumgen on a new local cluster, and we had trouble linking hdf5 library.
This line was giving us trouble:
mpicc -o build/pumgen -fopenmp -Wl,-rpath=/lrz/sys/libraries/netcdf/4.3.3/intel/ibmmpi_poe1.4_1505/lib (...) lSimPartitionWrapper-mpich2 -lSimModel -lpskernel
something like undefined reference to H5_Close
And actually we solved it adding -lhdf5 to this line. So maybe something has to be updated in the install script.
PUMGen fails with MPI abort error
Sun Sep 06 14:01:48, Warn: SimModeler: [433] Code: 60 String: General error
Rank 433 [Sun Sep 6 14:01:48 2020] [c0-3c0s13n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 433
Sun Sep 06 14:01:48, Warn: SimModeler: [966] Code: 60 String: General error
Rank 966 [Sun Sep 6 14:01:48 2020] [c3-3c1s4n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 966
Sun Sep 06 14:01:48, Warn: SimModeler: [984] Code: 60 String: General error
Rank 984 [Sun Sep 6 14:01:48 2020] [c3-3c1s9n1] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 984
Sun Sep 06 14:01:48, Warn: SimModeler: [688] Code: 60 String: General error
Rank 688 [Sun Sep 6 14:01:48 2020] [c1-3c2s5n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 688
Sun Sep 06 14:01:48, Warn: SimModeler: [856] Code: 60 String: General error
Rank 856 [Sun Sep 6 14:01:48 2020] [c2-3c2s5n0] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 856
Sun Sep 06 14:01:48, Warn: SimModeler: [675] Code: 60 String: General error
Rank 675 [Sun Sep 6 14:01:48 2020] [c1-3c2s2n2] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 675
Sun Sep 06 14:01:48, Warn: SimModeler: [592] Code: 60 String: General error
Rank 592 [Sun Sep 6 14:01:48 2020] [c1-3c0s10n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 592
Sun Sep 06 14:01:48, Warn: SimModeler: [650] Code: 60 String: General error
Rank 650 [Sun Sep 6 14:01:48 2020] [c1-3c1s11n1] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 650
Sun Sep 06 14:01:48, Warn: SimModeler: [658] Code: 60 String: General error
Rank 658 [Sun Sep 6 14:01:48 2020] [c1-3c1s13n1] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 658
Sun Sep 06 14:01:48, Warn: SimModeler: [655] Code: 60 String: General error
Rank 655 [Sun Sep 6 14:01:48 2020] [c1-3c1s12n2] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 655
Sun Sep 06 14:01:48, Warn: SimModeler: [668] Code: 60 String: General error
Rank 668 [Sun Sep 6 14:01:48 2020] [c1-3c1s15n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 668
Sun Sep 06 14:01:48, Warn: SimModeler: [667] Code: 60 String: General error
Rank 667 [Sun Sep 6 14:01:48 2020] [c1-3c1s15n2] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 667
Sun Sep 06 14:01:48, Warn: SimModeler: [664] Code: 60 String: General error
Rank 664 [Sun Sep 6 14:01:48 2020] [c1-3c1s14n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 664
Sun Sep 06 14:01:48, Warn: SimModeler: [682] Code: 60 String: General error
Rank 682 [Sun Sep 6 14:01:48 2020] [c1-3c2s4n1] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 682
Sun Sep 06 14:01:48, Warn: SimModeler: [842] Code: 60 String: General error
Rank 842 [Sun Sep 6 14:01:48 2020] [c2-3c2s1n2] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 842
Sun Sep 06 14:01:48, Warn: SimModeler: [853] Code: 60 String: General error
Rank 853 [Sun Sep 6 14:01:48 2020] [c2-3c2s4n1] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 853
Sun Sep 06 14:01:48, Warn: SimModeler: [605] Code: 60 String: General error
Sun Sep 06 14:01:48, Warn: SimModeler: [817] Code: 60 String: General error
PUMGEN fails with msh2, floating point exception
I get the following error when running pumgen with this command using a gmsh version 2 file.
pumgen t4.msh2 -s msh2
Tue Aug 02 20:04:58, Info: Using GMSH mesh format 2 (msh2) mesh
Tue Aug 02 20:04:58, Info: Create APF connectivity
Tue Aug 02 20:04:58, Info: Set coordinates in APF
Floating point exception (core dumped)
I attached the msh2 file which should be a valid file (renamed with .txt to allow upload to Github). I generated this file with the Gmsh Python package.
I use the pumgen executable here: /hppfs/work/pr63qo/di73yeq4/myLibs/PUMGen/build/pumgen on SuperMUC-NG.
Boundary conditions incorrectly set in bypass-apf branch
I'm generating a mesh with
https://github.com/SeisSol/Examples/blob/master/tpv5/generating_mirror_mesh.sh
And vizualizing the BC with:
python ~/SeisSol/Meshing/vizualizeBoundaryConditions/vizualizeBoundaryConditions.py tpv5_f200_halfdom.xdmf 0
I get with the bypass-apf branch
and the mesh64 branch
PCU_Switch_Comm requires valid MPI communicator
We cannot use MPI_UNDEFINED here because PCU requires a valid communicator:
Line 67 in b1661b8
Replacing MPI_UNDEFINED with 1 should do the trick.
compiling pumgen with spack on Ubuntu 22.04.2 LTS
I tried compiling PUMGen with spack without simmetrix on Ubuntu 22.04.2 and results in the following error:
Error: ProcessError: Command exited with status 1:
'/opt/spack/opt/spack/linux-ubuntu22.04-skylake/gcc-11.4.0/cmake-3.27.7-3eb3cedth3wunsstvc4dxs25o2r5wqcx/bin/cmake' '-G' 'Unix Makefiles'
>> 15 CMake Error at /opt/spack/opt/spack/linux-ubuntu22.04-skylake/gcc-11.4.0/cmake-3.27.7-3eb3cedth3wunsstvc4dxs25o2r5wqcx/share/cmake-3.27/Modules/FindHDF5.c
make:571 (get_target_property):
>> 33 CMake Error at /opt/spack/opt/spack/linux-ubuntu22.04-skylake/gcc-11.4.0/cmake-3.27.7-3eb3cedth3wunsstvc4dxs25o2r5wqcx/share/cmake-3.27/Modules/FindPackag
eHandleStandardArgs.cmake:230 (message):
34 Could NOT find HDF5 (missing: HL) (found version "1.12.2")
which can be reproduced:
spack install pumgen ~with_simmetrix
by the way, This worked a while ago, but why doesn't it work now.
PUMGen fails when writing a very large mesh
I get the following error when writing a very large mesh (684990261 cells):
log_file
(run on 15 ranks, with the mesh64 branch).
Currently Loaded Modulefiles:
1) paraview/5.11.1(default) 11) pigz/2.7-gcc-12.2.0-5w24zpq 21) pmix/4.2.3-gcc-12.2.0-ksjdukm 31) unzip/6.0-gcc-12.2.0-7wxq5cw
2) libpciaccess/0.17-gcc-12.2.0-foegz6x 12) zstd/1.5.5-gcc-12.2.0-d3iesv2 22) openmpi/4.1.5-gcc-12.2.0-ab5rikq 32) lua/5.3.2-gcc-12.2.0-zucnb2e
3) libiconv/1.17-gcc-12.2.0-pztn24l 13) tar/1.34-gcc-12.2.0-344crw2 23) pkgconf/1.9.5-gcc-12.2.0-pdjoat6 33) yaml-cpp/0.6.2-gcc-12.2.0-adem7ot
4) xz/5.4.1-gcc-12.2.0-beahnap 14) gettext/0.21.1-gcc-12.2.0-htnecfu 24) hdf5/1.12.2-gcc-12.2.0-xwxzdqa 34) easi/1.2.0-gcc-12.2.0-v2wqdbq
5) zlib/1.2.13-gcc-12.2.0-qvwbld7 15) openssl/3.1.1-gcc-12.2.0-xydqrfk 25) netcdf-c/4.7.4-gcc-12.2.0-5wzc2ic 35) simmetrix-simmodsuite/2023.0-230923-gcc-12.2.0-ybubb2z
6) libxml2/2.10.3-gcc-12.2.0-6g4ulfn 16) krb5/1.20.1-gcc-12.2.0-ywylqdh 26) asagi/1.0.1-gcc-12.2.0-xvz2l4l 36) metis/5.1.0-gcc-12.2.0-kcvzwx3
7) ncurses/6.4-gcc-12.2.0-bt2tv43 17) libedit/3.1-20210216-gcc-12.2.0-uybrqun 27) impalajit/main-gcc-12.2.0-judjtis 37) parmetis/4.0.3-gcc-12.2.0-minbyzl
8) hwloc/2.9.1-gcc-12.2.0-wjb3zv3 18) libxcrypt/4.4.35-gcc-12.2.0-bnemwrw 28) nghttp2/1.52.0-gcc-12.2.0-x5wdgxs 38) zoltan/3.83-gcc-12.2.0-sl2xogx
9) numactl/2.0.14-gcc-12.2.0-62dxa76 19) openssh/9.3p1-gcc-12.2.0-nvgsowj 29) curl/8.1.2-gcc-12.2.0-2s4wrx6 39) pumi/2.2.8-gcc-12.2.0-xud7zas
10) bzip2/1.0.8-gcc-12.2.0-yn6mmdj 20) libevent/2.1.12-gcc-12.2.0-zgp5wia 30) readline/8.2-gcc-12.2.0-ofdoevl 40) pumgen/mesh64-gcc-12.2.0-bjw5ufd
Apf Missing
Dear All,
I try to compile the new version of PUMGen, However, I got the following error:
-- Cray Programming Environment 2.6.5 C
-- NOTE: LOADEDMODULES changed since initial config!
-- NOTE: this may cause unexpected build errors.
-- Cray Programming Environment 2.6.5 CXX
CMake Warning (dev) at CMakeLists.txt:48 (find_package):
Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
Run "cmake --help-policy CMP0074" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
Environment variable HDF5_ROOT is set to:
/opt/cray/pe/hdf5-parallel/1.10.6.1/INTEL/19.1
For compatibility, CMake is ignoring the variable.
This warning is for project developers. Use -Wno-dev to suppress it.
-- HDF5: Using hdf5 compiler wrapper for all C compiling
-- Could NOT find APF (missing: APF_INCLUDE_DIR APF_LIBRARIES)
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/APF_INCLUDE_DIR
used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/APF_SIM_INCLUDE_DIR
used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/APF_ZOLTAN_INCLUDE_DIR
used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/GMI_INCLUDE_DIR
used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/GMI_SIM_INCLUDE_DIR
used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/LION_INCLUDE_DIR
used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/MA_INCLUDE_DIR
used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/MDS_INCLUDE_DIR
used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/MTH_INCLUDE_DIR
used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/PCU_INCLUDE_DIR
used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
APF_LIB
linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
APF_SIM_LIB
linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
APF_ZOLTAN_LIB
linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
GMI_LIB
linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
GMI_SIM_LIB
linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
LION_LIB
linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
MA_LIB
linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
MDS_LIB
linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
MTH_LIB
linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
PCU_LIB
linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
-- Configuring incomplete, errors occurred!
See also "/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/build/CMakeFiles/CMakeOutput.log".
make: *** No targets specified and no makefile found. Stop.
Here is my configuration:
mkdir build
cd build
/project/k1488/kadek/myLibs/cmakeSeisSol/bin/cmake/bin/cmake .. -DCMAKE_PREFIX_PATH=/project/k1488/kadek/myLibs/PUMGen_SeisSol/core/:/project/k1488/kadek/myLibs/cmakeSeisSol/lib/:/project/k1488/kadek/myLibs/cmakeSeisSol/bin/:/project/k1488/kadek/myLibs/cmakeSeisSol/include/:/project/k1488/kadek/myLibs/cmakeSeisSol/share/ -DSIMMETRIX=ON \
-DSIMMETRIX_ROOT=/project/k1488/kadek/myLibs/PUMGen_SeisSol/simmodeler/15.0-210501/ -DSIM_MPI=mpich3 \
-DCMAKE_BUILD_TYPE=Release\
-DCMAKE_C_COMPILER=cc -DCMAKE_CXX_COMPILER=CC
make -j 24
I don't understand with the Apf library. Could you please let me know what is wrong with my configuration?
Thank you for your help.
Best regards,
Kadek
installing PUMGen with cmake
Hi,
Today I tried to install PUMGen with cmake.
-
Do I need to manually set all the pumi/core lib and include path?
APF_SIM_LIB, APF_ZOLTAN_LIB, etc.
Can it be more simple? -
When generate with ccmake, I get the following warning:
WARNING: Target "pumgen" requests linking to directory "/hppfs/work/pr45fi/di73yeq4/myLibs/core/lib". Targets may link only to libraries. CMake is dropping the item.
does it mean I need to enter the name of each library, e.g. APF_SIM_LIB=/hppfs/work/pr45fi/di73yeq4/myLibs/core/libapf_sim.a
- The build fails when linking (maybe related to 2).
Scanning dependencies of target tinyxml2
[ 9%] Building CXX object CMakeFiles/tinyxml2.dir/submodules/tinyxml2/tinyxml2.cpp.o
[ 18%] Linking CXX static library libtinyxml2.a
[ 18%] Built target tinyxml2
Scanning dependencies of target pumgen
[ 27%] Building CXX object CMakeFiles/pumgen.dir/src/pumgen.cpp.o
[ 36%] Building CXX object CMakeFiles/pumgen.dir/src/meshreader/FidapReader.cpp.o
[ 45%] Building CXX object CMakeFiles/pumgen.dir/src/meshreader/GambitReader.cpp.o
[ 54%] Building CXX object CMakeFiles/pumgen.dir/src/input/SimModSuite.cpp.o
[ 63%] Building CXX object CMakeFiles/pumgen.dir/src/input/AnalysisAttributes.cpp.o
[ 72%] Building CXX object CMakeFiles/pumgen.dir/src/input/MeshAttributes.cpp.o
[ 81%] Building CXX object CMakeFiles/pumgen.dir/src/input/ParallelVertexFilter.cpp.o
[ 90%] Building CXX object CMakeFiles/pumgen.dir/src/input/split.cpp.o
[100%] Linking CXX executable pumgen
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: CMakeFiles/pumgen.dir/src/pumgen.cpp.o: in function `SerialMeshFile<puml::ParallelGambitReader>::open(char const*)':
pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x7a): undefined reference to `gmi_register_null'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x84): undefined reference to `gmi_load'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x93): undefined reference to `apf::makeEmptyMdsMesh(gmi_model*, int, bool)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x126): undefined reference to `apf::construct(apf::Mesh2*, int const*, int, int, std::map<int, apf::MeshEntity*, std::less<int>, std::allocator<std::pair<int const, apf::MeshEntity*> > >&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x13c): undefined reference to `apf::alignMdsRemotes(apf::Mesh2*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x145): undefined reference to `apf::deriveMdsModel(apf::Mesh2*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x19a): undefined reference to `apf::setCoords(apf::Mesh2*, double const*, int, std::map<int, apf::MeshEntity*, std::less<int>, std::allocator<std::pair<int const, apf::MeshEntity*> > >&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: CMakeFiles/pumgen.dir/src/pumgen.cpp.o: in function `ParallelFidapReader::readBoundaries(int*)':
pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x2c): undefined reference to `PCU_Comm_Begin'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x72): undefined reference to `PCU_Comm_Send'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x77): undefined reference to `PCU_Comm_Receive'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x94): undefined reference to `PCU_Comm_Unpack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xbc): undefined reference to `PCU_Comm_Unpack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xdc): undefined reference to `PCU_Comm_Receive'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x6c8): undefined reference to `PCU_Comm_Pack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x6d9): undefined reference to `PCU_Comm_Pack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x990): undefined reference to `PCU_Comm_Begin'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xa10): undefined reference to `PCU_Comm_Pack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xa3a): undefined reference to `PCU_Comm_Pack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xa51): undefined reference to `PCU_Comm_Send'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xa84): undefined reference to `PCU_Comm_Unpack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xa96): undefined reference to `PCU_Comm_Unpack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xac1): undefined reference to `PCU_Comm_Receive'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: CMakeFiles/pumgen.dir/src/pumgen.cpp.o: in function `SerialMeshFile<ParallelFidapReader>::open(char const*)':
pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x7a): undefined reference to `gmi_register_null'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x84): undefined reference to `gmi_load'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x93): undefined reference to `apf::makeEmptyMdsMesh(gmi_model*, int, bool)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x185): undefined reference to `apf::construct(apf::Mesh2*, int const*, int, int, std::map<int, apf::MeshEntity*, std::less<int>, std::allocator<std::pair<int const, apf::MeshEntity*> > >&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x19b): undefined reference to `apf::alignMdsRemotes(apf::Mesh2*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x1a4): undefined reference to `apf::deriveMdsModel(apf::Mesh2*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x1f9): undefined reference to `apf::setCoords(apf::Mesh2*, double const*, int, std::map<int, apf::MeshEntity*, std::less<int>, std::allocator<std::pair<int const, apf::MeshEntity*> > >&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: CMakeFiles/pumgen.dir/src/pumgen.cpp.o: in function `main':
pumgen.cpp:(.text.startup+0xa0): undefined reference to `PCU_Comm_Init'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0xfa2): undefined reference to `gmi_register_mesh'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0xfad): undefined reference to `apf::loadMdsMesh(char const*, char const*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0xfe0): undefined reference to `apf::alignMdsMatches(apf::Mesh2*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1079): undefined reference to `PCU_Comm_Self'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x111f): undefined reference to `gmi_write_dmg'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1176): undefined reference to `PCU_Comm_Self'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x11b2): undefined reference to `apf::writeVtkFiles(char const*, apf::Mesh*, int)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x11c1): undefined reference to `apf::countOwned(apf::Mesh*, int, apf::Sharing*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x11cf): undefined reference to `apf::countOwned(apf::Mesh*, int, apf::Sharing*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x12b7): undefined reference to `ma::getInsphere(apf::Mesh2*, apf::MeshEntity*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x13f7): undefined reference to `apf::numberOwnedNodes(apf::Mesh*, char const*, apf::FieldShape*, apf::Sharing*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1404): undefined reference to `apf::makeGlobal(apf::NumberingOf<int>*, bool)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1411): undefined reference to `apf::synchronize(apf::NumberingOf<long>*, apf::Sharing*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1686): undefined reference to `apf::getElementNumbers(apf::NumberingOf<long>*, apf::MeshEntity*, apf::NewArray<long>&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1894): undefined reference to `apf::getSharing(apf::Mesh*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1906): undefined reference to `apf::getNumber(apf::NumberingOf<long>*, apf::Node, int)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1957): undefined reference to `apf::Mesh::getPoint(apf::MeshEntity*, int, apf::Vector3&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x286d): undefined reference to `PCU_Comm_Free'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x2985): undefined reference to `gmi_register_null'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: CMakeFiles/pumgen.dir/src/pumgen.cpp.o: in function `SimModSuite::SimModSuite(char const*, char const*, char const*, char const*, char const*, int, char const*, char const*, bool, bool, char const*)':
pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x4ad): undefined reference to `apf::createMesh(PartitionedMesh*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x4b5): undefined reference to `gmi_register_sim()'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x4be): undefined reference to `gmi_import_sim(SGModel*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x506): undefined reference to `apf::createMdsMesh(gmi_model*, apf::Mesh*, bool, bool)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x512): undefined reference to `apf::destroyMesh(apf::Mesh*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x564): undefined reference to `apf::Mesh::getModelType(apf::ModelEntity*)'
collect2: error: ld returned 1 exit status
CMakeFiles/pumgen.dir/build.make:211: recipe for target 'pumgen' failed
make[2]: *** [pumgen] Error 1
CMakeFiles/Makefile2:72: recipe for target 'CMakeFiles/pumgen.dir/all' failed
make[1]: *** [CMakeFiles/pumgen.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2
APF_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/core/lib
APF_SIM_INCLUDE_DIR /hppfs/work/pr45fi/di73yeq4/myLibs/core/include
APF_SIM_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/core/lib
APF_ZOLTAN_INCLUDE_DIR /hppfs/work/pr45fi/di73yeq4/myLibs/core/include
APF_ZOLTAN_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/core/lib
BEFORE_SIM_11 OFF
BEFORE_SIM_14 OFF
CMAKE_BUILD_TYPE
CMAKE_INSTALL_PREFIX /hppfs/work/pr45fi/di73yeq4/myLibs/PUMGen/build_cmake
GMI_INCLUDE_DIR /hppfs/work/pr45fi/di73yeq4/myLibs/core/include
GMI_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/core/lib
GMI_SIM_INCLUDE_DIR /hppfs/work/pr45fi/di73yeq4/myLibs/core/include
GMI_SIM_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/core/lib
HDF5_C_LIBRARY_dl /usr/lib64/libdl.so
HDF5_C_LIBRARY_hdf5 /dss/dsshome1/lrz/sys/spack/release/19.2/opt/x86_avx512/hdf5/1.8.20-intel-mhsivcc/lib/libhdf5.so
HDF5_C_LIBRARY_hdf5_hl /dss/dsshome1/lrz/sys/spack/release/19.2/opt/x86_avx512/hdf5/1.8.20-intel-mhsivcc/lib/libhdf5_hl.so
HDF5_C_LIBRARY_m /usr/lib64/libm.so
HDF5_C_LIBRARY_pthread /usr/lib64/libpthread.so
HDF5_C_LIBRARY_sz /dss/dsshome1/lrz/sys/spack/release/19.2/opt/x86_avx512/libszip/2.1.1-gcc-v3th2mi/lib/libsz.so
HDF5_C_LIBRARY_z /dss/dsshome1/lrz/sys/spack/release/19.2/opt/x86_avx512/zlib/1.2.11-gcc-ajxhsmr/lib/libz.so
LION_INCLUDE_DIR /hppfs/work/pr45fi/di73yeq4/myLibs/core/include
LION_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/core/lib
LOG_LEVEL info
MA_INCLUDE_DIR /hppfs/work/pr45fi/di73yeq4/myLibs/core/include
MA_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/core/lib
MDS_INCLUDE_DIR /hppfs/work/pr45fi/di73yeq4/myLibs/core/include
MDS_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/core/lib
MESH_SIM_INCLUDE_DIR /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/include
MTH_INCLUDE_DIR /hppfs/work/pr45fi/di73yeq4/myLibs/core/include
MTH_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/core/lib
NETCDF OFF
PCU_INCLUDE_DIR /hppfs/work/pr45fi/di73yeq4/myLibs/core/include
PCU_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/core/lib
SIMMETRIX ON
SIMMETRIX_ROOT /hppfs/work/pr63qo/di73yeq4/myLibs/SimModelerLib/14.0-190921
SIM_ACIS_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/libSimAcis2017.a
SIM_DISCRETE_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/libSimDiscrete.a
SIM_EXPORT_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/libSimExport.a
SIM_MESHING_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/libSimMeshing.a
SIM_MESH_TOOLS_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/libSimMeshTools.a
SIM_MODEL_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/libSimModel.a
SIM_PARASOLID_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/libSimParasolid310.a
SIM_PARTITINED_WRAPPER_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/libSimPartitionWrapper-mpich3.a
SIM_PARTITIONED_MESH_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/libSimPartitionedMesh.a
SIM_PARTITIONED_MESH_MPI_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/libSimPartitionedMesh-mpi.a
SIM_PS_KRNL_LIB /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/psKrnl/libpskernel.so
Thomas.
PUMGen compilation and hdf5 on Shaheen
Hii All,
I am getting following error in PUMGen compilation on Shaheen. Any suggestion:
Currently Loaded Modulefiles:
- modules/3.2.11.4 12) intel/19.0.5.281 23) alps/6.6.58-7.0.1.1_6.8__g437d88db.ari
- craype-haswell 13) python/3.8.0-cdl 24) rca/2.2.20-7.0.1.1_4.51__g8e3fb5b.ari
- craype-network-aries 14) cray-libsci/19.06.1 25) atp/3.6.4
- craype/2.6.3 15) udreg/2.3.2-7.0.1.1_3.36__g8175d3d.ari 26) perftools-base/7.1.3
- cray-mpich/7.7.11 16) ugni/6.0.14.0-7.0.1.1_7.38__ge78e5b0.ari 27) PrgEnv-intel/6.0.5
- slurm/slurm 17) pmi/5.0.15 28) cmake/3.13.4
- dws/3.0.28-7.0.1.1_6.35__ge55277c.ari 18) dmapp/7.1.1-7.0.1.1_4.52__g38cf134.ari 29) scons/3.0.1
- eproxy/2.0.24-7.0.1.1_5.10__g45c478a.ari 19) gni-headers/5.0.12.0-7.0.1.1_6.31__g3b1768f.ari 30) cray-netcdf-hdf5parallel/4.6.3.2
- xalt/1.1.2 20) xpmem/2.2.20-7.0.1.1_4.13__g0475745.ari 31) cray-hdf5-parallel/1.10.5.2
- darshan/3.1.7 21) job/2.2.4-7.0.1.1_3.40__g36b56f4.ari 32) cray-tpsl/19.06.1
- ksl/ksl 22) dvs/2.12_2.2.157-7.0.1.1_9.4__g083131db
simModSuite=yes mpiLib=mpich3 netcdf=yes cc=/opt/cray/pe/craype/2.6.3/bin/cc cxx=/opt/cray/pe/craype/2.6.3/bin/CC logLevel=debug prefixPath=/home/vyasjc/meshing-soft-pumi-pumgen/PUMI/core:/home/vyasjc/meshing-soft-pumi-pumgen/simmetrix/14.0-200719:/home/vyasjc/meshing-soft-pumi-pumgen/parmetis-4.0.3/include:/home/vyasjc/TP-SeisSol/hdf5-1.8.21/build:/home/vyasjc/TP-SeisSol/netcdf-4.6.1/build
scons: Reading SConscript files ...
Checking for C++ library gmi_sim... yes
Checking for C++ library apf_sim... yes
Checking for C++ library apf_zoltan... yes
Checking for C++ library gmi... yes
Checking for C++ library mds... yes
Checking for C++ library ma... yes
Checking for C++ library apf... yes
Checking for C++ library pcu... yes
Checking for C++ library lion... yes
Checking for C++ library mth... yes
Checking whether h5pcc program exists...(cached) yes
IndexError: list index out of range:
File "/home/vyasjc/meshing-soft-pumi-pumgen/PUMGen/SConstruct", line 135:
libs.find(env, 'hdf5', required=True, parallel=True)
File "/home/vyasjc/meshing-soft-pumi-pumgen/PUMGen/site_scons/libs/init.py", line 43:
return lib_find(env, **kw);
File "/home/vyasjc/meshing-soft-pumi-pumgen/PUMGen/site_scons/libs/hdf5.py", line 103:
if not conf.CheckLibWithHeader(flags['LIBS'][0], 'hdf5.h', 'c', extra_libs=flags['LIBS'][1:]):
Converting mesh to APF fails for large mesh
I'm trying to generate a larger mesh for the texascale.
The mesh (750M cells) is created by pumgen, but there is then a bug with APF.
Might be a memory overflow, but we have 999Gb of RAM on the server (exception, and I was the only one using at the time).
I'm using the mesh64 branch, but this is not a new bug of this branch as I experienced it before.
(pumgen compiled with spack, with:
spack install pumgen@mesh64 +with_simmetrix ^[email protected] ^[email protected] ^easi jit=impalajit,lua (and the package modified so that it know the mesh64 version).
Sat Oct 07 13:09:41, Info: No filtering enabled (contiguous storage)
Sat Oct 07 13:09:41, Info: Using SimModSuite
Sat Oct 07 13:09:41, Info: Loading model
Sat Oct 07 13:11:58, Info: Extracting cases
Sat Oct 07 13:11:58, Info: surface smoothing option: surfaceSmoothingLevel surfaceSmoothingType surfaceFaceRotationLimit Snap 1 1 5 0
Sat Oct 07 13:11:58, Info: volume smoothing option: volumeSmoothingLevel volumeSmoothingType 1 1
Sat Oct 07 13:11:58, Info: Activating velocity aware meshing, using 2 elements per wavelength and easi file Mw_78_Turkey_rhomulambda1D_Guvercin_et_al.yaml
Sat Oct 07 13:11:58, Info: Adding velocity aware refinement region targeting 6 Hz, centered at x = 20000 y= 50000 z= -10000 with half sizes x = 200000 y = 100000 z = 15000
Sat Oct 07 13:11:58, Info: rotated around z axis by 45 degree(s) counterclockwise from x axis.
Sat Oct 07 13:11:58, Info: bypass findRegion and use group = 1
Sat Oct 07 13:11:58, Info: Adding velocity aware refinement region targeting 0.25 Hz, centered at x = 0 y= 0 z= -15000 with half sizes x = 4e+11 y = 1.5e+11 z = 1.5e+11
Sat Oct 07 13:11:58, Info: bypass findRegion and use group = 1
Sat Oct 07 13:11:58, Info: Setting cases
Sat Oct 07 13:11:58, Info: faceBound[ 96 ] = 1
Sat Oct 07 13:11:58, Info: faceBound[ 105 ] = 1
Sat Oct 07 13:11:58, Info: faceBound[ 95 ] = 5
Sat Oct 07 13:11:58, Info: faceBound[ 98 ] = 5
Sat Oct 07 13:11:58, Info: faceBound[ 107 ] = 5
Sat Oct 07 13:11:58, Info: faceBound[ 110 ] = 5
Sat Oct 07 13:11:58, Info: faceBound[ 119 ] = 5
Sat Oct 07 13:11:58, Info: faceBound[ 100 ] = 65
Sat Oct 07 13:11:58, Info: faceBound[ 93 ] = 66
Sat Oct 07 13:11:58, Info: faceBound[ 94 ] = 66
Sat Oct 07 13:11:58, Info: faceBound[ 108 ] = 66
Sat Oct 07 13:11:58, Info: faceBound[ 116 ] = 66
Sat Oct 07 13:11:58, Info: faceBound[ 121 ] = 66
Sat Oct 07 13:11:58, Info: faceBound[ 102 ] = 67
Sat Oct 07 13:11:58, Info: faceBound[ 109 ] = 67
Sat Oct 07 13:11:58, Info: faceBound[ 117 ] = 67
Sat Oct 07 13:11:58, Info: faceBound[ 111 ] = 68
Sat Oct 07 13:11:58, Info: faceBound[ 94 ] = 68
Sat Oct 07 13:11:58, Info: faceBound[ 112 ] = 69
Sat Oct 07 13:11:58, Info: globalMSize = 5000
Sat Oct 07 13:11:58, Info: face id: 100 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 93 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 94 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 108 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 116 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 121 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 102 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 109 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 117 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 111 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 94 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 112 , MSize = 200
Sat Oct 07 13:11:58, Info: face id: 105 , MSize = 900
Sat Oct 07 13:11:58, Info: Enabling velocity aware meshing
Sat Oct 07 13:11:58, Info: Target equivolume AspectRatio = 12
Sat Oct 07 13:11:58, Info: Target equiarea AspectRatio = 6
Sat Oct 07 13:11:58, Info: Starting the surface mesher
Sat Oct 07 13:11:58, Info: Progress: Surface Meshing
Sat Oct 07 13:29:02, Info: Progress: Adapting Mesh
Sat Oct 07 13:30:04, Info: Progress: Surface Mesh Improver
Sat Oct 07 13:30:04, Info: Progress: Surface Mesh Improvement , 0 / 2
Sat Oct 07 13:30:04, Info: Progress: Surface Mesh Improvement , 1 / 2
Sat Oct 07 13:30:04, Info: Progress: Surface Mesh Improvement , 2 / 2
Sat Oct 07 13:30:04, Info: Progress: Surface Mesh Improvement , done
Sat Oct 07 13:30:04, Info: Progress: Surface Smoothing , 0 / 100
Sat Oct 07 13:30:04, Info: Progress: Surface Smoothing , 16 / 100
Sat Oct 07 13:30:04, Info: Progress: Surface Smoothing , 32 / 100
Sat Oct 07 13:30:04, Info: Progress: Surface Smoothing , done
Sat Oct 07 13:30:04, Info: Progress: Fix Surface Intersections
Sat Oct 07 13:30:15, Info: Starting the volume mesher
Sat Oct 07 13:30:15, Info: Progress: Volume Meshing
Sat Oct 07 13:30:15, Info: Progress: Creating volume mesh
Sat Oct 07 13:49:58, Info: Progress: Adapting Mesh
Sat Oct 07 13:50:09, Info: Progress: Volume Mesh Improver
Sat Oct 07 13:50:09, Info: Progress: Volume Optimization
Sat Oct 07 13:50:30, Info: Progress: Volume Smoothing , 0 / 100
Sat Oct 07 13:50:32, Info: Progress: Volume Smoothing , 5 / 100
Sat Oct 07 13:50:35, Info: Progress: Volume Smoothing , 10 / 100
Sat Oct 07 13:50:37, Info: Progress: Volume Smoothing , 15 / 100
Sat Oct 07 13:50:39, Info: Progress: Volume Smoothing , 20 / 100
Sat Oct 07 13:50:42, Info: Progress: Volume Smoothing , 25 / 100
Sat Oct 07 13:50:44, Info: Progress: Volume Smoothing , 30 / 100
Sat Oct 07 13:50:47, Info: Progress: Volume Smoothing , 35 / 100
Sat Oct 07 13:50:49, Info: Progress: Volume Smoothing , 40 / 100
Sat Oct 07 13:50:51, Info: Progress: Volume Smoothing , 45 / 100
Sat Oct 07 13:50:53, Info: Progress: Volume Smoothing , 50 / 100
Sat Oct 07 13:50:55, Info: Progress: Volume Smoothing , 55 / 100
Sat Oct 07 13:50:57, Info: Progress: Volume Smoothing , 60 / 100
Sat Oct 07 13:50:59, Info: Progress: Volume Smoothing , 65 / 100
Sat Oct 07 13:51:01, Info: Progress: Volume Smoothing , 70 / 100
Sat Oct 07 13:51:03, Info: Progress: Volume Smoothing , 75 / 100
Sat Oct 07 13:51:05, Info: Progress: Volume Smoothing , 80 / 100
Sat Oct 07 13:51:06, Info: Progress: Volume Smoothing , 85 / 100
Sat Oct 07 13:51:08, Info: Progress: Volume Smoothing , 90 / 100
Sat Oct 07 13:51:11, Info: Progress: Volume Smoothing , 95 / 100
Sat Oct 07 13:52:09, Info: Progress: Volume Smoothing , done
Sat Oct 07 13:52:13, Info: AR statistics:
Sat Oct 07 13:52:22, Info: AR max: 19.1125
Sat Oct 07 13:52:22, Info: AR (target: < ~10):
Sat Oct 07 13:52:22, Info: [ 0.00 , 2.00 ): 593524
Sat Oct 07 13:52:22, Info: [ 2.00 , 4.00 ): 728855697
Sat Oct 07 13:52:22, Info: [ 4.00 , 6.00 ): 22308449
Sat Oct 07 13:52:22, Info: [ 6.00 , 10.00 ): 2083036
Sat Oct 07 13:52:22, Info: [ 10.00 , 20.00 ): 30302
Sat Oct 07 13:52:22, Info: [ 20.00 , 40.00 ): 0
Sat Oct 07 13:52:22, Info: [ 40.00 , 100.00 ): 0
Sat Oct 07 13:52:22, Info: [ 100.00 ,inf): 0
Sat Oct 07 13:52:24, Info: Converting mesh to APF
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 33 with PID 0 on node exception exited on signal 9 (Killed).
--------------------------------------------------------------------------
SConstruct in master branch
Dear All,
In the documentation, there is a way to compile with a scons, but there is no SConstruct in the main folder of master branch. Is this scons depreciated?
Thank you.
Best,
Kadek
.bashrc adjustment for pumgen command
Hi all,
how a .bashrc adjustment should be to make the pumgen command correctly work?
Thanks in advance.
Error while installing xml pumgen
Hi,
I got this error while compiling xml pumgen:
In file included from src/pumgen.cpp:38:
src/input/SimModSuite.h:557:12: error: no matching function for call to 'MS_setMeshSizePropagation'
MS_setMeshSizePropagation(meshCase,face,2,1,MeshAtt.MeshSizePropagationDistance,MeshAtt.MeshSizePropagationScalingFactor);
^~~~~~~~~~~~~~~~~~~~~~~~~
/project/k1343/palgunkh/myLibs/meshing_software/simmetrix/14.0-200424/include/MeshSim.h:149:21: note: candidate function not viable: requires 5 arguments, but 6 were provided
Meshing_EXPORT void MS_setMeshSizePropagation(pACase cs, pGEntity gent, int closure, double distance, double sizeFactor);
^
In file included from src/pumgen.cpp:38:
src/input/SimModSuite.h:566:92: warning: expression result unused [-Wunused-value]
logInfo(PMU_rank()) << "UseDiscreteMesh; faceid, noModification:"<<*it, MeshAtt.UseDiscreteMesh_noModification;
~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:631:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(ent = (pGEntity)PList_next(lsmallFeats,&iter)){
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:631:15: note: place parentheses around the assignment to silence this warning
while(ent = (pGEntity)PList_next(lsmallFeats,&iter)){
^
( )
src/input/SimModSuite.h:631:15: note: use '==' to turn this assignment into an equality comparison
while(ent = (pGEntity)PList_next(lsmallFeats,&iter)){
^
==
src/input/SimModSuite.h:642:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(vert = (pGVertex)PList_next(vertices,&iter2)){
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:642:20: note: place parentheses around the assignment to silence this warning
while(vert = (pGVertex)PList_next(vertices,&iter2)){
^
( )
src/input/SimModSuite.h:642:20: note: use '==' to turn this assignment into an equality comparison
while(vert = (pGVertex)PList_next(vertices,&iter2)){
^
==
src/input/SimModSuite.h:705:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (reg = RIter_next(reg_it)) {
~~~~^~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:705:20: note: place parentheses around the assignment to silence this warning
while (reg = RIter_next(reg_it)) {
^
( )
src/input/SimModSuite.h:705:20: note: use '==' to turn this assignment into an equality comparison
while (reg = RIter_next(reg_it)) {
^
==
src/input/SimModSuite.h:772:22: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(modelRegion=GRIter_next(modelRegions)) { // get the next model region
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:772:22: note: place parentheses around the assignment to silence this warning
while(modelRegion=GRIter_next(modelRegions)) { // get the next model region
^
( )
src/input/SimModSuite.h:772:22: note: use '==' to turn this assignment into an equality comparison
while(modelRegion=GRIter_next(modelRegions)) { // get the next model region
^
==
src/input/SimModSuite.h:787:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(modelFace=GFIter_next(modelFaces)) { // get the next model face
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:787:20: note: place parentheses around the assignment to silence this warning
while(modelFace=GFIter_next(modelFaces)) { // get the next model face
^
( )
src/input/SimModSuite.h:787:20: note: use '==' to turn this assignment into an equality comparison
while(modelFace=GFIter_next(modelFaces)) { // get the next model face
^
==
src/input/SimModSuite.h:819:21: warning: unused variable 'hasnorm' [-Wunused-variable]
int hasnorm = SimPolygons_pointData(poly, polypoint[k], pntlocation, pntnormal);
^
src/input/SimModSuite.h:761:12: warning: unused variable 'edgeList' [-Wunused-variable]
pPList edgeList; // Edges bounding a face
^
src/input/SimModSuite.h:762:12: warning: unused variable 'thisEdge' [-Wunused-variable]
pGEdge thisEdge;
^
9 warnings and 1 error generated.
scons: *** [build/src/pumgen.o] Error 1
scons: building terminated because of errors.
Do I miss something?
Thank you.
Cheers,
Kadek
Segmentation Fault when Converting a larger .neu File with PumGen
I've encountered another issue while attempting to convert a .neu file generated with SimModeler v2024.0-240519 using PumGen. The mesh is larger this time (about 28 GB), and it causes a segmentation fault in both the latest version and v1.0.1 of PumGen. I can provide the mesh if that would be helpful.
I compiled pumgen without simmetrix support using the following library versions:
I can run this with gdb or a debug build if you think it would be useful.
The program crashes during the conversion process with the following error output:
Wed Jul 24 12:18:19, Info: No filtering enabled (contiguous storage)
Wed Jul 24 12:18:19, Info: Using 32-bit integer boundary type conditions, or 8 bit per face (i32).
Wed Jul 24 12:18:19, Info: Using Gambit mesh
Wed Jul 24 12:18:19, Warn: Gambit format does not seem to have a fixed boundary line length. Trying with variable line length
Wed Jul 24 12:18:19, Warn: Gambit format does not seem to have a fixed boundary line length. Trying with variable line length
Wed Jul 24 12:18:19, Warn: Gambit format does not seem to have a fixed boundary line length. Trying with variable line length
Wed Jul 24 12:18:24, Info: Read vertex coordinates
Wed Jul 24 12:18:24, Info: Reading vertices part 1 of 1
Wed Jul 24 12:20:08, Info: Read cell vertices
Wed Jul 24 12:20:11, Info: Reading elements part 1 of 1
Wed Jul 24 12:26:10, Info: Read cell groups
Wed Jul 24 12:26:11, Info: Reading group information part 1 of 1
[cos-bmadden-dt:373731] *** Process received signal ***
[cos-bmadden-dt:373731] Signal: Segmentation fault (11)
[cos-bmadden-dt:373731] Signal code: Address not mapped (1)
[cos-bmadden-dt:373731] Failing at address: 0x16ed07f840
[cos-bmadden-dt:373731] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f4f9c9df520]
[cos-bmadden-dt:373731] [ 1] /home/017552119/PUMGen/pumgen/build/pumgen(+0x16455)[0x55cd30bc8455]
[cos-bmadden-dt:373731] [ 2] /home/017552119/PUMGen/pumgen/build/pumgen(+0x1779b)[0x55cd30bc979b]
[cos-bmadden-dt:373731] [ 3] /home/017552119/PUMGen/pumgen/build/pumgen(+0x1906d)[0x55cd30bcb06d]
[cos-bmadden-dt:373731] [ 4] /home/017552119/PUMGen/pumgen/build/pumgen(+0x976f)[0x55cd30bbb76f]
[cos-bmadden-dt:373731] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f4f9c9c6d90]
[cos-bmadden-dt:373731] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f4f9c9c6e40]
[cos-bmadden-dt:373731] [ 7] /home/017552119/PUMGen/pumgen/build/pumgen(+0xc025)[0x55cd30bbe025]
[cos-bmadden-dt:373731] *** End of error message ***
Segmentation fault (core dumped)
problem + solutions compiling pumgen
I had trouble compiling pumgen using mpi.intel/2017 on my desktop.
Basically at linking, I got:
(base) ulrich@tegern:/export/data/ulrich/MyLibs/PUMGen$ mpicxx -o build/pumgen -fopenmp -Wl,-rpath=/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib -Wl,-rpath=/export/data/ulrich/MyLibs/core/build/lib build/src/pumgen.o build/src/input/ParallelVertexFilter.o build/src/meshreader/GambitReader.o build/src/meshreader/FidapReader.o -L/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib -L/export/data/ulrich/MyLibs/core/build/lib -lapf_zoltan -lgmi -lmds -lma -lapf -lpcu -llion -lmth -lhdf5
/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib/libhdf5.a(H5.o): In function `H5_term_library':
H5.c:(.text+0xcb): undefined reference to `__intel_sse2_strlen'
H5.c:(.text+0x11c): undefined reference to `__intel_sse2_strlen'
H5.c:(.text+0x190): undefined reference to `__intel_sse2_strlen'
H5.c:(.text+0x1e1): undefined reference to `__intel_sse2_strlen'
H5.c:(.text+0x27c): undefined reference to `__intel_sse2_strlen'
Which turned out to the fact that mpicxx uses by default g++ and not icpc.
(base) ulrich@tegern:/export/data/ulrich/MyLibs/PUMGen$ mpicxx
This script invokes an appropriate specialized C++ MPI compiler driver.
The following ways (priority order) can be used for changing default
compiler name (g++):
1. Command line option: -cxx=<compiler_name>
2. Environment variable: I_MPI_CXX (current value '')
3. Environment variable: MPICH_CXX (current value '')
therefore I added -cxx=icpc which brought me to the next problem:
(base) ulrich@tegern:/export/data/ulrich/MyLibs/PUMGen$ mpicxx -cxx=icpc -o build/pumgen -fopenmp -Wl,-rpath=/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib -Wl,-rpath=/export/data/ulrich/MyLibs/core/build/lib build/src/pumgen.o build/src/input/ParallelVertexFilter.o build/src/meshreader/GambitReader.o build/src/meshreader/FidapReader.o -L/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib -L/export/data/ulrich/MyLibs/core/build/lib -lapf_zoltan -lgmi -lmds -lma -lapf -lpcu -llion -lmth -lhdf5
/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib/libhdf5.a(H5Zdeflate.o): In function `H5Z_filter_deflate':
H5Zdeflate.c:(.text+0xcc): undefined reference to `inflateInit_'
H5Zdeflate.c:(.text+0xe2): undefined reference to `inflate'
H5Zdeflate.c:(.text+0x1dd): undefined reference to `compress2'
H5Zdeflate.c:(.text+0x305): undefined reference to `inflateEnd'
H5Zdeflate.c:(.text+0x345): undefined reference to `inflateEnd'
H5Zdeflate.c:(.text+0x39a): undefined reference to `inflateEnd'
Which I solved adding '-lz' to the command
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