atomisticnet / aenet Goto Github PK

The error messages are listed below:

mpif90 -c -DPARALLEL -O2 -pedantic -fexternal-blas parallel.F90 -o parallel.o
parallel.F90:1603:23:

1603 | call MPI_allreduce(buff, val, 1, MPI_DOUBLE_PRECISION, MPI_SUM, &
| 1
......
1623 | call MPI_allreduce(buff, val, n, MPI_DOUBLE_PRECISION, MPI_SUM, &
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
parallel.F90:1584:23:

1584 | call MPI_allreduce(buff, val, n, MPI_INTEGER, MPI_SUM, &
| 1
......
1623 | call MPI_allreduce(buff, val, n, MPI_DOUBLE_PRECISION, MPI_SUM, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/REAL(8)).
parallel.F90:1564:23:

1564 | call MPI_allreduce(buff, val, 1, MPI_INTEGER, MPI_SUM, &
| 1
......
1623 | call MPI_allreduce(buff, val, n, MPI_DOUBLE_PRECISION, MPI_SUM, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/REAL(8)).
parallel.F90:1469:21:

1469 | call MPI_Recv(val, 1, MPI_LOGICAL, src, tag, &
| 1
......
1531 | call MPI_Recv(val, nm, MPI_CHARACTER, src, tag, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (LOGICAL(4)/CHARACTER()).
parallel.F90:1472:21:

1472 | call MPI_Recv(val, 1, MPI_LOGICAL, MPI_ANY_SOURCE, &
| 1
......
1531 | call MPI_Recv(val, nm, MPI_CHARACTER, src, tag, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (LOGICAL(4)/CHARACTER()).
parallel.F90:1442:21:

1442 | call MPI_Recv(val, n, MPI_DOUBLE_PRECISION, src, tag, &
| 1
......
1531 | call MPI_Recv(val, nm, MPI_CHARACTER, src, tag, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/CHARACTER()).
parallel.F90:1445:21:

1445 | call MPI_Recv(val, n, MPI_DOUBLE_PRECISION, MPI_ANY_SOURCE, &
| 1
......
1531 | call MPI_Recv(val, nm, MPI_CHARACTER, src, tag, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/CHARACTER()).
parallel.F90:1414:21:

1414 | call MPI_Recv(val, 1, MPI_DOUBLE_PRECISION, src, tag, &
| 1
......
1531 | call MPI_Recv(val, nm, MPI_CHARACTER, src, tag, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/CHARACTER()).
parallel.F90:1417:21:

1417 | call MPI_Recv(val, 1, MPI_DOUBLE_PRECISION, MPI_ANY_SOURCE, &
| 1
......
1531 | call MPI_Recv(val, nm, MPI_CHARACTER, src, tag, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/CHARACTER()).
parallel.F90:1387:21:

1387 | call MPI_Recv(val, n, MPI_INTEGER, src, tag, &
| 1
......
1531 | call MPI_Recv(val, nm, MPI_CHARACTER, src, tag, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/CHARACTER()).
parallel.F90:1390:21:

1390 | call MPI_Recv(val, n, MPI_INTEGER, MPI_ANY_SOURCE, &
| 1
......
1531 | call MPI_Recv(val, nm, MPI_CHARACTER, src, tag, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/CHARACTER()).
parallel.F90:1359:21:

1359 | call MPI_Recv(val, 1, MPI_INTEGER, src, tag, &
| 1
......
1531 | call MPI_Recv(val, nm, MPI_CHARACTER, src, tag, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/CHARACTER()).
parallel.F90:1362:21:

1362 | call MPI_Recv(val, 1, MPI_INTEGER, MPI_ANY_SOURCE, &
| 1
......
1531 | call MPI_Recv(val, nm, MPI_CHARACTER, src, tag, &
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/CHARACTER()).
parallel.F90:1278:18:

1278 | call MPI_Send(val, 1, MPI_LOGICAL, dest, tag, MPI_COMM_WORLD, ierr)
| 1
......
1328 | call MPI_Send(val, mn, MPI_CHARACTER, dest, tag, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (LOGICAL(4)/CHARACTER()).
parallel.F90:1257:18:

1257 | call MPI_Send(val, n, MPI_DOUBLE_PRECISION, dest, tag, MPI_COMM_WORLD, ierr)
| 1
......
1328 | call MPI_Send(val, mn, MPI_CHARACTER, dest, tag, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/CHARACTER()).
parallel.F90:1235:18:

1235 | call MPI_Send(val, 1, MPI_DOUBLE_PRECISION, dest, tag, MPI_COMM_WORLD, ierr)
| 1
......
1328 | call MPI_Send(val, mn, MPI_CHARACTER, dest, tag, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/CHARACTER()).
parallel.F90:1214:18:

1214 | call MPI_Send(val, n, MPI_INTEGER, dest, tag, MPI_COMM_WORLD, ierr)
| 1
......
1328 | call MPI_Send(val, mn, MPI_CHARACTER, dest, tag, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/CHARACTER()).
parallel.F90:1192:18:

1192 | call MPI_Send(val, 1, MPI_INTEGER, dest, tag, MPI_COMM_WORLD, ierr)
| 1
......
1328 | call MPI_Send(val, mn, MPI_CHARACTER, dest, tag, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/CHARACTER()).
parallel.F90:1103:22:

1103 | call MPI_Bcast(val, n, MPI_LOGICAL, root, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (LOGICAL(4)/CHARACTER(*)).
parallel.F90:1105:22:

1105 | call MPI_Bcast(val, n, MPI_LOGICAL, 0, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (LOGICAL(4)/CHARACTER(*)).
parallel.F90:1079:22:

1079 | call MPI_Bcast(val, 1, MPI_LOGICAL, root, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (LOGICAL(4)/CHARACTER(*)).
parallel.F90:1081:22:

1081 | call MPI_Bcast(val, 1, MPI_LOGICAL, 0, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (LOGICAL(4)/CHARACTER(*)).
parallel.F90:1056:22:

1056 | call MPI_Bcast(val, n, MPI_DOUBLE_PRECISION, root, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/CHARACTER(*)).
parallel.F90:1058:22:

1058 | call MPI_Bcast(val, n, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/CHARACTER(*)).
parallel.F90:1032:22:

1032 | call MPI_Bcast(val, 1, MPI_DOUBLE_PRECISION, root, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/CHARACTER(*)).
parallel.F90:1034:22:

1034 | call MPI_Bcast(val, 1, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/CHARACTER(*)).
parallel.F90:1009:22:

1009 | call MPI_Bcast(val, n, MPI_INTEGER, root, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/CHARACTER(*)).
parallel.F90:1011:22:

1011 | call MPI_Bcast(val, n, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/CHARACTER(*)).
parallel.F90:985:22:

985 | call MPI_Bcast(val, 1, MPI_INTEGER, root, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/CHARACTER(*)).
parallel.F90:987:22:

987 | call MPI_Bcast(val, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)
| 1
......
1159 | call MPI_Bcast(val, m, MPI_CHARACTER, root, MPI_COMM_WORLD, ierr)
| 2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/CHARACTER(*)).
make: *** [parallel.o] Error 1

I am reading the source code of fingerprint calculation. In line 817 of
src/ext/sfbasis.f90

f = chebyshev_polynomial(cos_ijk, 0.0d0, PI, sfb%a_order)

chebyshev_polynomial takes cos_ijk as input and cos_ijk is from

cos_ijk = dot_product(R_ij, R_ik)/(d_ij*d_ik)

The cosine value ranges from -1 to 1, but in line 817, [0.0, PI] is used. Is there any special concerns for this? Besides, why not use radian instead of cosine?

There are several instances in lclist.f90 where the value of a potentially uninitialized variable itype is accessed:

 if ( (.not. present(itype)) .or. (atomType(iatom) == itype)) then

Affected lines in lclist.f90: 432, 459, 578, 611

Is it possible for aenet to do training on energies and forces? It is not obvious how to specify that in the input files if so.

Hello, I want to use aenet to train a model, I see fingerprint.f90 can compute the structural fingerprints.
While, when I use it with a dir including some xsf file, it report a "segment fault" error. When I use it with one xsf file, it will generate some results, not a stp file. How to use it?
Thanks a lot.

As follows:

$$$$ ./fingerprint.x xsf/structure10000136911.xsf 6.5 12 6.5 4 Ti O
xsf/structure10000136911.xsf 75
xsf/structure10000136911.xsf 75
xsf/structure10000136911.xsf 74
xsf/structure10000136911.xsf 74
xsf/structure10000136911.xsf 70
xsf/structure10000136911.xsf 78
xsf/structure10000136911.xsf 73
xsf/structure10000136911.xsf 78
xsf/structure10000136911.xsf 73
xsf/structure10000136911.xsf 73
xsf/structure10000136911.xsf 77
xsf/structure10000136911.xsf 76
xsf/structure10000136911.xsf 1.42661317E+01 1.48715715E+00 -1.10546093E+01 -2.17259282E+00 5.09528968E+00 6.81191796E-02 -1.23834783E+00 1.48251178E+00 -1.43082665E-01 -1.34007727E+00 2.51005362E-01 4.36856773E-01 1.17738736E-01 9.89171875E+01 -1.00225288E+02 1.29628481E+02 -2.65745459E+02 6.70475042E+02 -4.83391464E+00 -3.57385843E-01 3.70342088E+00 4.06425929E-01 -1.64218313E+00 1.56185631E-01 3.10252400E-01 -2.78981747E-01 2.03700063E-01 5.25495597E-02 -5.75246723E-02 6.51295891E-02 -5.73658127E-01 9.05182379E+00 -8.11461593E+00 7.67151255E+00 -1.42835689E+01 3.89613732E+01

$$$$$$ ./fingerprint.x xsf/ 6.5 12 6.5 4 Ti O
Segmentation fault

Hi, I have built an mpi version of aenet via:

make -f makefiles/Makefile.gfortran_mpi

As far as I can see it worked fine, and I have a new train.x-2.0.3-gfortran_mpi executable. It is not obvious to me it does anything in parallel though. If I run it like this:

mpirun -np 6 train.x-2.0.3-gfortran_mpi train.in

I can't tell that it is running on 6 cores, and only energies.test.0 and energies.train.0 are created (I thought perhaps 6 of them might be created).

Is there anything you need to put in the input file, or other thing that is required to run aenet in parallel? Thanks,

I followed all the process in the documentation for the installation. I installed the python interface using -- python setup install --user

But when I try to import ANNCalculator using from aenet.ase_calculator import ANNCalculator in the python script, I get the following error: "core.cpython-36m-x86_64-linux-gnu.so: undefined symbol: AENET_ERR_MALLOC"

I tried to compile aenet using gfortran_serial and gfortran_mpi, both are giving the same issue.

Also, does the python interface only work for python3 ?

Please help me how to solve this problem, thank you for your help in advance.

ahmadfaisalharish@Ahmads-MacBook-Pro ~ % cd Downloads
ahmadfaisalharish@Ahmads-MacBook-Pro Downloads % cd aenet-master
ahmadfaisalharish@Ahmads-MacBook-Pro aenet-master % cd lib
ahmadfaisalharish@Ahmads-MacBook-Pro lib % make
gcc -shared Lbfgsb.3.0/blas_pic.o Lbfgsb.3.0/lbfgsb_pic.o Lbfgsb.3.0/linpack_pic.o Lbfgsb.3.0/timer_pic.o -lm -lgfortran -o liblbfgsb.so
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [liblbfgsb.so] Error 1

In an earlier version there was a Python interface that allowed one to use an aenet trained potential in ASE. It seems to be missing in this version. Do you know if the older version still works with this?

Hello,
I compile aenet with intel fortran compiler.
but during install process,
python for using ase don't set up.

here for my code with error
$ python3.9 setup.py build_ext --inplace

running build_ext
skipping 'aenet/core.c' Cython extension (up-to-date)
building 'aenet.core' extension
gcc -pthread -B /usr/local/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /usr/local/miniconda3/include -fPIC -O2 -isystem /usr/local/miniconda3/include -fPIC -I/home/chkim/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/miniconda3/include/python3.9 -c aenet/core.c -o build/temp.linux-x86_64-3.9/aenet/core.o -I../src -I./aenet -fPIC -O2
In file included from /home/chkim/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:0,
from /home/chkim/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/chkim/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5,
from aenet/core.c:701:
/home/chkim/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with "
^
aenet/core.c:2908:27: warning: ‘__pyx_f_5aenet_4core__chars’ defined but not used [-Wunused-function]
static __Pyx_memviewslice __pyx_f_5aenet_4core__chars(PyObject *__pyx_v_s) {
^
gcc -pthread -B /usr/local/miniconda3/compiler_compat -Wl,--sysroot=/ -shared -Wl,-rpath,/usr/local/miniconda3/lib -Wl,-rpath-link,/usr/local/miniconda3/lib -L/usr/local/miniconda3/lib -Wl,-rpath,/usr/local/miniconda3/lib -Wl,-rpath-link,/usr/local/miniconda3/lib -L/usr/local/miniconda3/lib build/temp.linux-x86_64-3.9/aenet/core.o ../lib/Lbfgsb.3.0/blas_pic.o ../lib/Lbfgsb.3.0/lbfgsb_pic.o ../lib/Lbfgsb.3.0/linpack_pic.o ../lib/Lbfgsb.3.0/timer_pic.o -llapack -lblas -lifort -o /home/chkim/aenet/python3/aenet/core.cpython-39-x86_64-linux-gnu.so
/usr/local/miniconda3/compiler_compat/ld: cannot find -llapack
/usr/local/miniconda3/compiler_compat/ld: cannot find -lblas
/usr/local/miniconda3/compiler_compat/ld: cannot find -lifort
collect2: error: ld returned 1 exit status
error: command '/usr/bin/gcc' failed with exit code 1

I think it is an error for using intel's
Could you help how i doing for this problem??

After compiling aenet successfully, I followed the instructions in the README.rst in the python3/ folder to install aenet-predict.py and aenet-md.py. I used the following commands:

$ cd ../src
$ make -f ./makefiles/Makefile.XXX lib
$ cd -
$ python setup.py build_ext --inplace

and when I try and run aenet-md.py I get the following error which looks like something has gone wrong in using cython for the ANNPotentials class:

Traceback (most recent call last):
  File "/u/fs1/afh41/.conda/envs/ml-tools/bin/aenet-predict.py", line 4, in <module>
    __import__('pkg_resources').run_script('aenet==0.1.0a1', 'aenet-predict.py')
  File "/u/fs1/afh41/.conda/envs/ml-tools/lib/python3.7/site-packages/pkg_resources/__init__.py", line 667, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/u/fs1/afh41/.conda/envs/ml-tools/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1464, in run_script
    exec(code, namespace, namespace)
  File "/home/users/afh41/.local/lib/python3.7/site-packages/aenet-0.1.0a1-py3.7-linux-x86_64.egg/EGG-INFO/scripts/aenet-predict.py", line 40, in <module>
    from aenet.ase_calculator import ANNCalculator
  File "/u/fs1/afh41/.local/lib/python3.7/site-packages/aenet-0.1.0a1-py3.7-linux-x86_64.egg/aenet/ase_calculator.py", line 24, in <module>
    from aenet.core import ANNPotentials
ImportError: /u/fs1/afh41/.local/lib/python3.7/site-packages/aenet-0.1.0a1-py3.7-linux-x86_64.egg/aenet/core.cpython-37m-x86_64-linux-gnu.so: undefined symbol: mpi_comm_rank_