Welcome to the forums. Please post in English or French.

You are not logged in.

#1 2020-09-10 13:20:16

sameer21101970
Member
Registered: 2019-09-06
Posts: 199

code_aster 14.4 parallel version with PETSc - Mumps error & further he

Mumps installation while compiling MPI version with Petsc has below error, Can Anybody pointout where i am might be going wrong. i am following  hitoricae.com/2019/11/10/code_aster-14-4-with-petsc/  link

$ make all
make ARITH=c mumps_lib
make[1]: Entering directory '/home/sameer/Install_Files/opt/mumps-5.1.2_mob'
(cd src ; make c)
make[2]: Entering directory '/home/sameer/Install_Files/opt/mumps-5.1.2_mob/src'
make ARITH=c mumps_lib
make[3]: Entering directory '/home/sameer/Install_Files/opt/mumps-5.1.2_mob/src'
mpif90 -O -fPIC -DPORD_INTSIZE64 -fopenmp -I/opt/aster/public/metis-5.1.0/include -I/opt/parmetis-4.0.3/include -I/opt/scotch-6.0.4/include -I/opt/aster/public/metis-5.1.0/include -I/opt/parmetis-4.0.3/include -I/opt/scotch-6.0.4/include -Dpord -Dmetis -Dparmetis -Dscotch -Dptscotch -I. -I../include -c ana_orderings_wrappers_m.F -o ana_orderings_wrappers_m.o
f951: Warning: Nonexistent include directory ‘/opt/scotch-6.0.4/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/opt/scotch-6.0.4/include’ [-Wmissing-include-dirs]
ana_orderings_wrappers_m.F:371: Error: Can't open included file 'scotchf.h'
Makefile:293: recipe for target 'ana_orderings_wrappers_m.o' failed
make[3]: *** [ana_orderings_wrappers_m.o] Error 1
make[3]: Leaving directory '/home/sameer/Install_Files/opt/mumps-5.1.2_mob/src'
Makefile:20: recipe for target 'c' failed
make[2]: *** [c] Error 2
make[2]: Leaving directory '/home/sameer/Install_Files/opt/mumps-5.1.2_mob/src'
Makefile:40: recipe for target 'mumps_lib' failed
make[1]: *** [mumps_lib] Error 2
make[1]: Leaving directory '/home/sameer/Install_Files/opt/mumps-5.1.2_mob'
Makefile:18: recipe for target 'c' failed
make: *** [c] Error 2

Offline

#2 2020-09-10 22:16:02

Irvise
Member
Registered: 2019-12-07
Posts: 20

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Here is the key of your error:

f951: Warning: Nonexistent include directory ‘/opt/scotch-6.0.4/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/opt/scotch-6.0.4/include’ [-Wmissing-include-dirs]
ana_orderings_wrappers_m.F:371: Error: Can't open included file 'scotchf.h'

The scotch directory the build is referencing does not exist.

I have given the guide a quick look. The scoth build is just right before the mups one. Make sure that you have done the scotch build successfully and that the /opt/scotch-6.0.4/include exist.

Regards,

Fer

Offline

#3 2020-09-11 07:34:13

sameer21101970
Member
Registered: 2019-09-06
Posts: 199

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

scotch 6.0.4 already build in Install_Files/opt/

have install files as under. hope, steps also point out what i have done wrong.

make folder - Install_Files
mkdir opt in above folder

In Install_Files Folder following files where Extract & install as per procedure set
a. OpenBlas 3.10
b. aster_full src 14.4.0
c. parmetis 4.03
d. scalapack_installer

Now, in Folder
Install_Files/opt
following files were extracted and install as per procedure set
a. scotch6.0.4 ( copied .gz file from aster full 14.04 )
b. mumps 5.1.2_mob ( name changed ) ( coped .gz file from aster full 14.04)

while installing mumps above error shown.

kindly reply any step of installation missing out.

Offline

#4 2020-09-12 19:29:53

Irvise
Member
Registered: 2019-12-07
Posts: 20

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Hi.

The compile line:

mpif90 -O -fPIC -DPORD_INTSIZE64 -fopenmp -I/opt/aster/public/metis-5.1.0/include -I/opt/parmetis-4.0.3/include -I/opt/scotch-6.0.4/include -I/opt/aster/public/metis-5.1.0/include -I/opt/parmetis-4.0.3/include -I/opt/scotch-6.0.4/include -Dpord -Dmetis -Dparmetis -Dscotch -Dptscotch -I. -I../include -c ana_orderings_wrappers_m.F -o ana_orderings_wrappers_m.o

Is looking for files under the \opt directory. This directory is absolute, meaning it is the \opt directory that lives under \. The "\opt" directory you are referring to is a local (or better said, relative) directory that lives under "/home/sameer/Install_Files/opt".

The quickest and easiest way to fix this would be by redoing all the compilation under the expected directory: the \opt directory. There may be a way to indicate the make command to use a different directory to look for the libraries, but that would require manual intervention. I am not saying this would be a difficult thing to do, but it will require quite a bit more debugging since it will most likely not work on the first try.

Regards,
Fer

Offline

#5 2020-09-14 12:17:51

sameer21101970
Member
Registered: 2019-09-06
Posts: 199

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Ok. Have started installing with your given instructions but got stuck with petsc-3.9.4.tar.gz...installing hypre.
github path to installation Hypre doesnot exist.

./configure --with-debugging=0 COPTFLAGS=-O CXXOPTFLAGS=-O FOPTFLAGS=-O --with-shared-libraries=0 --with-scalapack-dir=/opt/scalapack-n --PETSC_ARCH=linux-metis-mumps --with-metis-dir=/opt/aster/public/metis-5.1.0 --with-parmetis-dir=/opt/parmetis-4.0.3 --with-ptscotch-dir=/opt/scotch-6.0.4 --LIBS="-lgomp" --with-mumps-dir=/opt/mumps-5.1.2_mob -with-x=0 --with-blas-lapack-lib=[/opt/OpenBLAS/lib/libopenblas.a] --download-hypre=yes --download-ml=yes

on repeating above command below config.log file shows details

Last edited by sameer21101970 (2020-09-14 12:28:39)

Offline

#6 2020-09-14 12:37:47

sameer21101970
Member
Registered: 2019-09-06
Posts: 199

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

check below attach file

Offline

#7 2020-09-14 12:53:11

sameer21101970
Member
Registered: 2019-09-06
Posts: 199

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

#endif
*******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
-------------------------------------------------------------------------------
Unable to run git stash/clean in repository: /opt/petsc-3.9.4/linux-metis-mumps/externalpackages/git.ml.
Perhaps its a git error!
*******************************************************************************
  File "./config/configure.py", line 394, in petsc_configure
    framework.configure(out = sys.stdout)
  File "/opt/petsc-3.9.4/config/BuildSystem/config/framework.py", line 1092, in configure
    self.processChildren()
  File "/opt/petsc-3.9.4/config/BuildSystem/config/framework.py", line 1081, in processChildren
    self.serialEvaluation(self.childGraph)
  File "/opt/petsc-3.9.4/config/BuildSystem/config/framework.py", line 1062, in serialEvaluation
    child.configure()
  File "/opt/petsc-3.9.4/config/BuildSystem/config/package.py", line 864, in configure
    self.executeTest(self.configureLibrary)
  File "/opt/petsc-3.9.4/config/BuildSystem/config/base.py", line 127, in executeTest
    ret = test(*args,**kargs)
  File "/opt/petsc-3.9.4/config/BuildSystem/config/package.py", line 753, in configureLibrary
    for location, directory, lib, incl in self.generateGuesses():
  File "/opt/petsc-3.9.4/config/BuildSystem/config/package.py", line 355, in generateGuesses
    d = self.checkDownload()
  File "/opt/petsc-3.9.4/config/BuildSystem/config/package.py", line 481, in checkDownload
    return self.getInstallDir()
  File "/opt/petsc-3.9.4/config/BuildSystem/config/package.py", line 294, in getInstallDir
    self.updateGitDir()
  File "/opt/petsc-3.9.4/config/BuildSystem/config/package.py", line 574, in updateGitDir
    raise RuntimeError('Unable to run git stash/clean in repository: '+self.packageDir+'.\nPerhaps its a git error!')
================================================================================
Finishing configure run at Mon, 14 Sep 2020 16:56:34 +0530
================================================================================

Offline

#8 2020-09-16 08:04:27

sameer21101970
Member
Registered: 2019-09-06
Posts: 199

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Running make install on ML; this may take several minutes                                                               ===============================================================================                                               **************************************************************************************************                            Please register to use hypre at computation.llnl.gov/casc/linear_solvers/sls_hypre.html                               **************************************************************************************************                            ===============================================================================                                                     Trying to download git:// github.com/LLNL/hypre for HYPRE         

github.com/LLNL/hypre/archive/v2.14.0.tar.gz is not a tarball

github has removed above link

where to download hypre manually and rerun terminal command

Offline

#9 2020-09-16 15:06:07

sameer21101970
Member
Registered: 2019-09-06
Posts: 199

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

hypre manually added...

but have further problem

asrun not read...error as under.

Checking measure of VmSize during MPI_Init : ok 
Checking for library pthread             : yes
Checking for library dl                  : yes
Checking for library util                : yes
Checking for program 'python'            : /usr/bin/python3
Checking for python version >= 3.5.0     : 3.6.9
python-config                            : /usr/bin/python3-config
Asking python-config for pyembed '--cflags --libs --ldflags' flags : yes
Testing pyembed configuration            : yes
Asking python-config for pyext '--cflags --libs --ldflags' flags : yes
Testing pyext configuration              : yes
Checking for numpy                       : /home/sameer/.local/lib/python3.6/site-packages/numpy/__init__.py
Checking for numpy version               : 1.19.2
Checking for numpy include               : ['/home/sameer/.local/lib/python3.6/site-packages/numpy/core/include']
Checking for asrun                       : Could not find the python module 'asrun'
(complete log in /home/sameer/Install_Files/aster-full-src-14.4.0/SRC/aster-14.4.0/build/std/config.log)




#include <Python.h>
#include <numpy/arrayobject.h>

int main(int argc, char **argv) {
    (void)argc; (void)argv;
    return 0;
}

<==
[1/2] Compiling [32mbuild/std/.conf_check_d1e8da006504a519a3971608c01ca992/test.cpp[0m

['mpicxx', '-g', '-fdebug-prefix-map=/build/python3.6-npOuKa/python3.6-3.6.9=.', '-fstack-protector', '-g', '-fwrapv', '-O3', '-I../../../../../../../../../.local/lib/python3.6/site-packages/numpy/core/include', '-I/opt/petsc-3.9.4/linux-metis-mumps/include', '-I/opt/petsc-3.9.4/include', '-I/ usr / include / superlu', '-I/opt/parmetis-4.0.3/include', '-I/opt/mumps-5.1.2_mob/include', '-I/opt/aster/public/hdf5-1.10.3/include', '-I/opt/aster/public/med-4.0.0/include', '-I/opt/aster/public/metis-5.1.0/include', '-I/opt/scotch-6.0.4/include', '-I/opt/scalapack-n/include', '-I/opt/OpenBLAS/include', '-I/usr/include/python3.6m', '-DHAVE_MPI=1', '-D_USE_MPI=1', '-D_USE_OPENMP=1', '-DENABLE_PROC_STATUS=1', '-DPYTHONDIR="/opt/aster/PAR14.4MUPT/lib/python3.6/site-packages"', '-DPYTHONARCHDIR="/opt/aster/PAR14.4MUPT/lib/python3.6/site-packages"', '-DHAVE_PYEMBED=1', '-DHAVE_PYEXT=1', '-DNPY_NO_PREFIX', '-DNDEBUG', '../../test.cpp', '-c', '-o/home/sameer/Install_Files/aster-full-src-14.4.0/SRC/aster-14.4.0/build/std/.conf_check_d1e8da006504a519a3971608c01ca992/testbuild/release/test.cpp.1.o']
err: In file included from ../../../../../../../../../.local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0,
                 from ../../../../../../../../../.local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from ../../../../../../../../../.local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from ../../test.cpp:2:
../../../../../../../../../.local/lib/python3.6/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 " \
  ^~~~~~~

[2/2] Linking [33mbuild/std/.conf_check_d1e8da006504a519a3971608c01ca992/testbuild/release/testprog[0m

['mpicxx', '-Xlinker', '-export-dynamic', '-Wl,-O1', '-Wl,-Bsymbolic-functions', 'test.cpp.1.o', '-o/home/sameer/Install_Files/aster-full-src-14.4.0/SRC/aster-14.4.0/build/std/.conf_check_d1e8da006504a519a3971608c01ca992/testbuild/release/testprog', '-Wl,-Bstatic', '-Wl,-Bdynamic', '-L/opt/petsc-3.9.4/linux-metis-mumps/lib', '-L/opt/parmetis-4.0.3/lib', '-L/opt/mumps-5.1.2_mob/lib', '-L/opt/aster/public/hdf5-1.10.3/lib', '-L/opt/aster/public/med-4.0.0/lib', '-L/opt/aster/public/metis-5.1.0/lib', '-L/opt/scotch-6.0.4/lib', '-L/opt/scalapack-n/lib', '-L/opt/OpenBLAS/lib', '-L/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu', '-L/usr/lib', '-lX11', '-lpthread', '-ldl', '-lutil', '-lpython3.6m', '-lpthread', '-ldl', '-lutil', '-lm', '-lpython3.6m', '-lpthread', '-ldl', '-lutil', '-lm']
['/home/sameer/.local/lib/python3.6/site-packages/numpy/core/include']
----------------------------------------
Checking for asrun
['/usr/bin/python3', '-c', "\nimport asrun as current_module\nversion = getattr(current_module, '__version__', None)\nif version is not None:\n\tprint(str(version))\nelse:\n\tprint('unknown version')\n"]
err: Traceback (most recent call last):
  File "<string>", line 2, in <module>
ModuleNotFoundError: No module named 'asrun'

from /home/sameer/Install_Files/aster-full-src-14.4.0/SRC/aster-14.4.0: Could not find the python module 'asrun'

Offline

#10 2020-09-16 22:04:45

Irvise
Member
Registered: 2019-12-07
Posts: 20

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Hi.

Could you post the contents of this file? (complete log in /home/sameer/Install_Files/aster-full-src-14.4.0/SRC/aster-14.4.0/build/std/config.log) The issue seems to be that it cannot find the python module/file known as asrun.

On another note, Hypre has changed its github, right now it is github.com/hypre-space/hypre the build scripts will need to be updated. However, I do not know who is responsible in this case.

Regards,

Fer

Offline

#11 2020-09-17 07:15:06

sameer21101970
Member
Registered: 2019-09-06
Posts: 199

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

kindly refer attach log file.


Attachments:
config.log, Size: 97.69 KiB, Downloads: 11

Offline

#12 2020-09-18 07:29:39

sameer21101970
Member
Registered: 2019-09-06
Posts: 199

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

waiting for reply.

Request CA Developers to include Petsc as available in standard Download of CA new version. Contact problems require Petsc.

Last edited by sameer21101970 (2020-09-18 13:08:27)

Offline

#13 2020-09-20 18:48:29

Irvise
Member
Registered: 2019-12-07
Posts: 20

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Hi Sameer,

after taking a look at the complete .log, my conclusion is the same. CA has a python module known as "asrun". During the build process, a few checks are done to make sure that all the dependencies are met before compiling CA. This is where it is failing, the system is unable to find the python module "asrun".

I am not very well versed with the python module system and how it works. I suppose that the "asrun" module is present somewhere the CA source folder. However, the python interpreter of your system "/usr/bin/python3" is not able to find it. My best guess is that the build script  is not exporting the PATH where "asrun" is present and therefore, the system fails to import it.

I am sadly unable to help you any further. Regards,

Fernando

Offline

#14 2020-09-21 07:15:33

sameer21101970
Member
Registered: 2019-09-06
Posts: 199

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Hello Fernando,

Yes you are right asrun is folder and it do exist in /opt/aster/lib/python3.6/site-packages/asrun

exportPath is not reading in my computer.

I Tried to Install CA Parallel on my Laptop, It Accepted asrun but AS HYPRE  IS INSTALLED MANUALLY the last step $ ./waf install -p --jobs=1 FAILED to Install and it has All Hypre Errors.

So, Some Expert from CA can Fix the Original Script with New Hypre Installation Address.

Offline

#15 Today 09:25:06

linctus
Member
Registered: 2011-11-02
Posts: 9

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

For asrun module not found issue, you have to set environment variables before ./waf configure

export ASTER_ROOT=where you install aster
export PYTHONPATH=$ASTER_ROOT/lib/python3.6/site-packages:$PYTHONPATH
./waf configure ....

For Hypre issue, you can try to compile petsc again letting it download hypre thing rather than MANUAL installation.
What you need to do is to modify the hypre repository in this file:

petsc-3.9.4/config/BuildSystem/config/packages/hypre.py

In this file, change

self.download  = ['git://https://github.com/LLNL/hypre','https://github.com/LLNL/hypre/archive/'+self.gitcommit+'.tar.gz']

to

self.download  = ['git://https://github.com/hypre-space/hypre','https://github.com/hypre-space/hypre/archive/'+self.gitcommit+'.tar.gz']

Hope this helps.

Online