trilinos / trilinos.github.io

Trilinos Project Homepage

Trilinos

Website | Documentation | Mailing List | Packages

The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.

Documentation

• Getting Started with Trilinos

• General Documentation

• Quick configure, build and install hints for Trilinos

• Trilinos Configure, Build, Test, and Install Reference Guide

• To ensure appropriate parties receive your issues, please direct issues by mentioning the Trilinos package owners. External users may not mention Github teams, but may mention individual owners instead.

• For help with a particular package, see the website and accompanying documentation for that package. Links to these can be found down the right side of any page on the website and at the package website.

License

Trilinos is licensed on a per-package basis. Most packages are now under a BSD license, some are published under the (L)GPL. Details can be taken from the documentation of each package.

Contributing

We appreciate your willingness to contribute to the Trilinos project. Please familiarize yourself with our contributing guidelines.

trilinos.github.io's Issues

Unit test fails because of missing HDF5

When building Trilinos 12.14.1, I get the error

error: ‘HDF5’ was not declared in this scope.

in Trilinos-trilinos-release-12-14-1/packages/epetraext/test/inout/EpetraExt_HDF5_UnitTest.cpp

I have configures Trilinos with

cmake .. -DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON \ -DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON \ -DTrilinos_ENABLE_Gtest:BOOL=ON \ -DTrilinos_ENABLE_TESTS=ON \ -DTPL_ENABLE_gtest:BOOL=ON \ -DTPL_ENABLE_MPI:BOOL=ON \ -DPYTHON_EXECUTABLE:PATH=/usr/bin/python2 \ -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DBUILD_SHARED_LIBS:BOOL=ON make VERBOSE=1

and HDF5 is not added automatically.

I'll now try to build explicitly with HDF5.Still, I think that the EpetraEx HDF5 unit test should be disabled if HDF5 is not added as a third partly library

Materials on old site Trilinos

In the trilinos.org, we have a lot of materials come from trilinos.org/oldsite. Most of these materials are pdf files and images. This is an example. Do you also want to move them to the new site? @maherou @jwillenbring. Thank you.

Regard "trilinos.sandia.gov" problem

In Trilinos website, there is many links in trilinos.sandia.gov that is not working anymore and will redirect into trilinos.org. Here is an example:
http://trilinos.sandia.gov/packages/docs/dev/packages/didasko/doc/html/index.html.
Do you have any idea on handling these links? Thank you @maherou, @jwillenbring

Belos: what's the best web page to point prospective users to?

@srajama1 @trilinos/belos

@cgcgcg and I will be doing a hands-on lecture at ATPESC in early August that will involve Belos and MueLu. Participants (mostly grad students) will be pointed to the package home pages for more information. Is https://trilinos.github.io/belos.html the best and most up-to-date reference link? Thanks.

New classification of packages on trilinos.github.io is incorrect

CC: @maherou, @jwillenbring, @rppawlo

I just noticed that the "Packages" drop-down at the top of:

• https://trilinos.github.io/

Now shows them partitioned into several different categories:

• MPI+X Packages
• MPI-Only Packages
• Research Packages
• Archive Packages

I am not sure who came up with the selection of packages in those lists but they are not consistent. Here are some examples of consistencies:

• Panzer is listed under "MPI+X Packages" build Phalanx is listed under "Research Packages". But Panzer has a required dependence on Phalanx so would Panzer not need to be listed as a "Research" package?
• Belos and Anasazi are listed under "MPI+X Packages" but Thyra, Stratimikos, NOX, LOCA, etc. are listed under "MPI-Only Packages". That makes zero sense. These are all just Abstract Numerical Algorithms (ANAs) that case use any underlying threaded or accelerated implementation. If Thyra is listed under "MPI-Only Packages" then Belos and Anasazi should be as well.
• ROL is listed under "MPI+X Packages" yet still can't fully run on a GPU. If Thyra is listed as "MPI-Only" then so should ROL.
• RTOp (not RTOP) is listed under "Archive Packages" but Thyra has a required dependence on RTOp so it can't be consider an archive package if Thyra is not considered an Archive package. Yet "TriUtils" is not listed under "Archive Packages". That is not consistent.
• Why is ForTrilinos even listed? It is not even in Trilinos. And how is that not a research package?

Problem checking out trilinos.github.io because of data quota

I was trying to clone trilinos.github.io on a new laptop. But ran into the following issue. The clone completed, but git-lfs failed. Maybe it is an issue with my environment, but I can't get past the this issue.

Here is output:

SJNBCSCI94119M:trilinos.github.io mheroux$ git checkout -f HEAD
Downloading download_files/trilinos-11.10.2-Source.tar.bz2 (111 MB)
Error downloading object: download_files/trilinos-11.10.2-Source.tar.bz2 (d3a39b7): Smudge error: Error downloading download_files/trilinos-11.10.2-Source.tar.bz2 (d3a39b7ad5c61d1e1413f9e550f0a81832a36e4a3072b8b99cebed6900d2d0ea): batch response: This repository is over its data quota. Purchase more data packs to restore access.

Errors logged to /Users/mheroux/repos/trilinos/trilinos.github.io/.git/lfs/logs/20180407T033010.058857522.log
Use `git lfs logs last` to view the log.
error: external filter 'git-lfs filter-process' failed
fatal: download_files/trilinos-11.10.2-Source.tar.bz2: smudge filter lfs failed

Trilinos (Kokkos) on MSVC (Visual Studio 19) and ICC

Hi team,
I am trying to compile entire Trilinos suite under MSVC(+ICC). Right now I managed to compile Kokkos + OpenMP but this came with quite a substantial effort and coding that raised many questions.

Basically we've found some issue that I would like to discuss before (possibly) submitting the emended code.

1. Kokkos_HostBarrier.cpp Line 103. The function try_wait(void) calls the static function try_wait(int *, const int, const int) passing non-static members (m_buffer...). Problem is: HostBarrier methods are often called by their static methods (e.g Kokkos_HostThreadTeam.hpp, line 139).

This, of course, is a clear error and I am surprised on how GCC could overcome this.

2. cas128_t is defined twice (Kokkos_AtomicAssembly.hpp and Kokkos_AtomicWindows.hpp) Solved this by removing definition in Kokkos_AtomicAssembly.hpp but I am not sure what the differences are.

3. atomic_compare_exchange with cas128_t (Impl::cas128_t atomic_compare_exchange<) has a conversion error: tmp.t = dest; Indeed it is trying to convert a pointer to cas128_t to cas128_t. Solved with tmp.t = *dest;

4. atomic_compare_exchange with SFINAE generates quite a lot of redefinition errors. Solved this by removing all SFINAE definitions and adding proper specialized bodies.

So, I am not sure if what we considered as errors are actual errors. Are we doing right with the proposed fixes (with those fixes we managed to compile Kokkos on Windows)?

Thank you in advance,
Alessio

Share available TUG slides?

Please consider this a feature request rather than a bug. The newest TUG tutorial slides I was able to find online were from 2014. Would it be possible to post newer TUG slides on the website?

Update/Remove Teams Page

This page is horrendously out of date: https://trilinos.github.io/team.html. Need to update or remove it.

TUG 2017 page in trilinos.github.io

Hi @maherou @jwillenbring,

I notice that two of you make some changes for the TUG 2017 page. Do you want me to make any changes for the webpage, such as the logo because I see that you try to update the logo multiple times.

Documentation on old sites

There are some documentations on old sites such as https://trilinos.org/docs/files/TrilinosBuildReference.html. Do you need to move them into our new site? @maherou @jwillenbring

Organize Packages Drop-down menu best understandability and usability

The Packages drop-down menu was recently re-organized to provide the reader with some guidance as to:

• The primary functionality of the package (only indicated in the MPI+X package list for now).
• The package execution model (MPI-only, MPI+X). Only those packages that are truly production quality.
• Indicate the present and future value of a package.

While the current names and groupings are an improvement of the previous single list of package names, there may be a better way to organize and classify the packages.

This issue is intended for capturing ideas and defining a how to improve the organization.

Trilinos user email list links are broken

At the mail lists page on trilinos.github.io, the links to the Trilinos user and announce email lists are broken. I'd fix this, but I have no idea what the correct links are anymore.

@maherou

Problem with netcdf when compiling Trilinos

Hello,

 I am trying to install Trilinos 12.17 in my local cluster.

 After successfully generating with cmake, I proceed on compiling, but I get errors like these:

 ex_put_variable_param.c:(.text+0x2e8): undefined reference to `nc_def_dim'
 ex_utils.c:(.text+0x2fad): undefined reference to `nc_put_att_float'

Investigating, I learned that they are due to bad linking or referencing to NetCDF. But, I do have NetDCF installed, netcdf-c-4.7.3.
When building Trilinos, I do:

-DTPL_Netcdf_LIBRARIES='/home/Felipe/BIGSOFTWARE/netcdf-c-4.7.3'
-DNetcdf_INCLUDE_DIRS='/home/Felipe/BIGSOFTWARE/netcdf-c-4.7.3/include'

and all good, it builds. The error comes with the compiling, when doing the 'make install'
I am doing; make -j8 && ctest -j8 && make -j8 install

What should I do?
Should I run a test on my netcdf?
Should I check for linking from Trilinos directory? is there any other better way to link? maybe the 'library dirs' needs to be more specific, but inside netcdf folder there are many subfolders whose name start with lib.. (such as libsrc, libserp, liblib, libdap..)

I would appreciate your help, as I do not know what to do.
Felipe

Petsc

How does Trtilinos decide to pick up petsc? I don't have it anywhere in my cmake specification, yet petsc libraries show up during the make stage.

What's more;, the wrong petsc libraries show up, despite me trying to put the right petsc in the environment.

I'm better that's why my make crashes

/opt/apps/intel18/impi/18.0.2/bin/mpicxx  -g -xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -mkl -DMPICH_SKIP_MPICXX -std=c++11 -O3 -DNDEBUG   CMakeFiles/Intrepid_test_Discretization_FunctionSpaceTools_Test_0\
5.dir/test_05.cpp.o  -o Intrepid_test_Discretization_FunctionSpaceTools_Test_05.exe  -Wl,-rpath,/tmp/trilinos-build/packages/intrepid/src:/tmp/trilinos-build/packages/pamgen/src:/tmp/trilinos-build/packa\
ges/amesos/src:/tmp/trilinos-build/packages/epetraext/src:/tmp/trilinos-build/commonTools/gtest:/tmp/trilinos-build/packages/shards/src:/tmp/trilinos-build/packages/sacado/src:/tmp/trilinos-build/package\
s/triutils/src:/opt/apps/intel18/impi18_0/phdf5/1.10.4/x86_64/lib:/tmp/trilinos-build/packages/epetra/src:/tmp/trilinos-build/packages/teuchos/kokkoscomm/src:/tmp/trilinos-build/packages/teuchos/kokkosco\
mpat/src:/tmp/trilinos-build/packages/teuchos/remainder/src:/tmp/trilinos-build/packages/teuchos/numerics/src:/tmp/trilinos-build/packages/teuchos/comm/src:/tmp/trilinos-build/packages/teuchos/parameterl\
ist/src:/tmp/trilinos-build/packages/teuchos/parser/src:/tmp/trilinos-build/packages/teuchos/core/src:/tmp/trilinos-build/packages/kokkos/core/src:/tmp/trilinos-build/packages/common/auxiliarySoftware/Su\
iteSparse/src ../../../src/libintrepid.so.12.18.1 ../../../../pamgen/src/libpamgen_extras.so.12.18.1 ../../../../pamgen/src/libpamgen.so.12.18.1 ../../../../amesos/src/libamesos.so.12.18.1 ../../../../ep\
etraext/src/libepetraext.so.12.18.1 ../../../../../commonTools/gtest/libgtest.so.12.18.1 ../../../../shards/src/libshards.so.12.18.1 ../../../../sacado/src/libsacado.so.12.18.1 ../../../../triutils/src/l\
ibtriutils.so.12.18.1 /opt/apps/intel18/impi18_0/phdf5/1.10.4/x86_64/lib/libhdf5.so /usr/lib64/libz.so /opt/apps/intel18/impi18_0/phdf5/1.10.4/x86_64/lib/libhdf5_hl.so ../../../../epetra/src/libepetra.so\
.12.18.1 ../../../../teuchos/kokkoscomm/src/libteuchoskokkoscomm.so.12.18.1 ../../../../teuchos/kokkoscompat/src/libteuchoskokkoscompat.so.12.18.1 ../../../../teuchos/remainder/src/libteuchosremainder.so\
.12.18.1 ../../../../teuchos/numerics/src/libteuchosnumerics.so.12.18.1 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread ../../../../teuchos/c\
omm/src/libteuchoscomm.so.12.18.1 ../../../../teuchos/parameterlist/src/libteuchosparameterlist.so.12.18.1 ../../../../teuchos/parser/src/libteuchosparser.so.12.18.1 ../../../../teuchos/core/src/libteuch\
oscore.so.12.18.1 ../../../../kokkos/core/src/libkokkoscore.so.12.18.1 /usr/lib64/libdl.so ../../../../common/auxiliarySoftware/SuiteSparse/src/libtrilinosss.so.12.18.1 -lm /home1/apps/intel18/impi18_0/p\
etsc/3.12/skylake/lib/libdmumps.a /home1/apps/intel18/impi18_0/petsc/3.12/skylake/lib/libmumps_common.a /home1/apps/intel18/impi18_0/petsc/3.12/skylake/lib/libpord.a
/admin/build/admin/rpms/stampede2/BUILD/trilinos-12.18.1/packages/percept/src/percept/function/StringFunction.cpp(488): (col. 5) remark: _ZN7percept14StringFunctionclERN8Intrepid14FieldContainerIdLi0EEES\
4_RKN3stk4mesh6BucketERKS3_d has been targeted for automatic cpu dispatch
/admin/build/admin/rpms/stampede2/BUILD/trilinos-12.18.1/packages/kokkos/core/src/Kokkos_View.hpp(2263): (col. 5) remark: _ZN6Kokkos4ViewIPxJNS_11LayoutRightENS_6DeviceINS_6SerialENS_9HostSpaceEEEvEEC1IA\
23_cEERKT_NSt9enable_ifIXsr6Kokkos4Impl13is_view_labelISA_EE5valueEKmE4typeEmmmmmmm has been targeted for automatic cpu dispatch
/opt/apps/gcc/6.3.0/include/c++/6.3.0/bits/vector.tcc(451): (col. 5) remark: _ZNSt6vectorIiSaIiEE14_M_fill_insertEN9__gnu_cxx17__normal_iteratorIPiS1_EEmRKi has been targeted for automatic cpu dispatch
/opt/apps/gcc/6.3.0/include/c++/6.3.0/bits/stl_algobase.h(750): (col. 5) remark: _ZSt10__fill_n_aIPdmdEN9__gnu_cxx11__enable_ifIXsr3std11__is_scalarIT1_EE7__valueET_E6__typeES4_T0_RKS3_ has been targeted\
 for automatic cpu dispatch
/opt/apps/gcc/6.3.0/include/c++/6.3.0/bits/stl_algobase.h(750): (col. 5) remark: _ZSt10__fill_n_aIPimiEN9__gnu_cxx11__enable_ifIXsr3std11__is_scalarIT1_EE7__valueET_E6__typeES4_T0_RKS3_ has been targeted\
 for automatic cpu dispatch
/opt/apps/gcc/6.3.0/include/c++/6.3.0/bits/stl_algobase.h(693): (col. 5) remark: _ZSt8__fill_aIPiiEN9__gnu_cxx11__enable_ifIXsr3std11__is_scalarIT0_EE7__valueEvE6__typeET_S6_RKS3_ has been targeted for a\
utomatic cpu dispatch
/opt/apps/gcc/6.3.0/include/c++/6.3.0/bits/stl_algobase.h(750): (col. 5) remark: _ZSt10__fill_n_aIPdldEN9__gnu_cxx11__enable_ifIXsr3std11__is_scalarIT1_EE7__valueET_E6__typeES4_T0_RKS3_ has been targeted\
 for automatic cpu dispatch
/admin/build/admin/rpms/stampede2/BUILD/trilinos-12.18.1/packages/kokkos/core/src/Kokkos_View.hpp(2263): (col. 5) remark: _ZN6Kokkos4ViewIPmJNS_10LayoutLeftENS_6DeviceINS_6SerialENS_9HostSpaceEEENS_12Mem\
oryTraitsILj0EEEEEC1IA22_cEERKT_NSt9enable_ifIXsr6Kokkos4Impl13is_view_labelISC_EE5valueEKmE4typeEmmmmmmm has been targeted for automatic cpu dispatch
/opt/apps/gcc/6.3.0/include/c++/6.3.0/bits/stl_vector.h(294): (col. 7) remark: _ZNSt6vectorIxSaIxEEC1EmRKxRKS0_ has been targeted for automatic cpu dispatch
/admin/build/admin/rpms/stampede2/BUILD/trilinos-12.18.1/packages/percept/src/percept/function/StringFunction.cpp(60): (col. 5) remark: _ZN7percept14StringFunction4initEv has been targeted for automatic \
cpu dispatch
../../../../amesos/src/libamesos.so.12.18.1: undefined reference to `blacs_gridinfo_'
../../../../amesos/src/libamesos.so.12.18.1: undefined reference to `scotchfgraphexit_'
../../../../amesos/src/libamesos.so.12.18.1: undefined reference to `scotchfstratdgraphorder_'
../../../../amesos/src/libamesos.so.12.18.1: undefined reference to `pdpotrf_'
../../../../amesos/src/libamesos.so.12.18.1: undefined reference to `pdgetrs_'
../../../../amesos/src/libamesos.so.12.18.1: undefined reference to `ParMETIS_V3_NodeND'
../../../../amesos/src/libamesos.so.12.18.1: undefined reference to `blacs_gridexit_'
../../../../amesos/src/libamesos.so.12.18.1: undefined reference to `METIS_PartGraphKway'
../../../../amesos/src/libamesos.so.12.18.1: undefined reference to `metis_setdefaultoptions_'
../../../../amesos/src/libamesos.so.12.18.1: undefined reference to `scotchfstratinit_'
../../../../amesos/src/libamesos.so.12.18.1: undefined reference to `scotchfstratexit_'

Trilinos Cmake Reference Link Broken

At https://trilinos.github.io/getting_started.html, clicking Trilinos CMake Reference gives a "This page no longer exists" error.

Starting page: link to Trilinos GitHub project is misleading

On the start page of trilinos.github.io, there's a button labelled with "View project on GitHub":

The label on this button indicates, that it will lead to the Trilinos source code repository, however it actually ends up here in the trilinos.github.io repository. This might be the reason, why Trilinos source code specific issues are sometimes opened in the wrong issue board.

Should this link be redirected to https://github.com/trilinos/Trilinos?

Create product area

We need an area in the website that replaces capability areas with product areas. Create a products folder under pages with an overview MD page and five product pages:

• framework
• data
• linear
• nonlinear
• discretizations

where can i find the Belos example

I want to sue Belos to solve my linear problems. Could you please tell me where to find the tutorial of Belos.
Regards

Interfacing STRUMPACK/ButterflyPACK

STRUMPACK/ButterflyPack team at LBL are asking where their code should be interfaced to Trilinos. Originally, they are thinking about contributing to Amesos2, but the intended use is preconditioner. In this case, adding an interface to other Trilinos package sounds more reasonable. I need your advice!

STRUMPACK
https://github.com/pghysels/STRUMPACK
ButterflyPack
https://github.com/liuyangzhuan/ButterflyPACK

Remove irrelevant pages and content

The trilinos.github.io site has a lot of out-of-date content. We need to systematically modify or remove it.

Correct warnings in examples and tests

Please refer to the following Trilinos pull request: trilinos/Trilinos#2364

@prwolfe

Please add tags for the releases

It is currently unclear how to download a specific version as the source files got removed from https://trilinos.org/oldsite/download/files/ and there are no tags here.

Please tag each release with a version

Table format in Trilinos user meeting

In Trilinos User Group Meeting 2007, Trilinos User Group Meeting 2008, Trilinos User Group Meeting 2009 and Trilinos User Group Meeting 2010, the tables are not well formatted. Do you want me to fix it? @maherou, @jwillenbring

Update MueLu documentation

MueLu's documentation is out of date.

What is the plan for this trilinos.github.io site?

Seems like it would be a lot of work to replace the current trilinos.org WordPress site. Is this just an experimentation or is there a real plan to make this transition? And if so, what is the timeline plan for that?

Remove non-working/misleading download links

As pointed out in trilinos/Trilinos#7260, the Trilinos github.io page has dead or misleading download links:

1. https://trilinos.github.io/download-12-0.html
2. Links on page https://trilinos.github.io/download-older.html

It would be good if users were always referred to the github release page.

Update Release Doxygen links to include only the latest release

We are going to discontinue support for Doxygen for release versions of Trilinos older than the most recent version. This is easier from a server perspective, and will prevent issues that some have observed with google searches turning up obsolete versions of documentation.

The links on the github.io site need to be updated to point to only the most recent release Doxygen version.

Done: Package Doxygen pages include links to only the most recent release, and the side bars include the latest release instead of 12.12.