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[OpenFOAM.com] Install OpenFOAM v1906 on a cluster with CentOS/RHEL 7

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Old   August 21, 2019, 02:37
Default Install OpenFOAM v1906 on a cluster with CentOS/RHEL 7
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zhenhai zhang
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Hey guys


I am trying to install the openFOAM on the university cluster and i have been following this link for reference.



https://www.openfoam.com/download/install-source.php


and every thing seems right until i run the command: foamInstallationTest and this is the error message displayed saying 'icoFoam not installed: (i apologize for the bad formatting of the post, it is actually my first post)

Code:

Basic setup :
-------------------------------------------------------------------------------
OpenFOAM:            OpenFOAM-v1906
ThirdParty:          ThirdParty-v1906
Shell:               bash
Host:                monarch-login2
OS:                  Linux version 3.10.0-957.5.1.el7.x86_64
-------------------------------------------------------------------------------


Main OpenFOAM env variables :
-------------------------------------------------------------------------------
EnvironmentVariable   FileOrDirectory                          Valid      Crit
-------------------------------------------------------------------------------
$WM_PROJECT_USER_DIR  /home/zzha518/OpenFOAM/zzha518-v1906      no        no
$WM_THIRD_PARTY_DIR   ...y81/zzha518/OpenFOAM/ThirdParty-v1906  yes       yes
-------------------------------------------------------------------------------


OpenFOAM env variables in PATH :
-------------------------------------------------------------------------------
EnvironmentVariable   FileOrDirectory                          Valid Path Crit
-------------------------------------------------------------------------------
$WM_PROJECT_DIR       .../ny81/zzha518/OpenFOAM/OpenFOAM-v1906  yes  yes  yes

$FOAM_APPBIN          ...06/platforms/linux64GccDPInt32Opt/bin  no        yes
$FOAM_SITE_APPBIN     ...06/platforms/linux64GccDPInt32Opt/bin  no        no
$FOAM_USER_APPBIN     ...06/platforms/linux64GccDPInt32Opt/bin  no        no
$WM_DIR               ...zzha518/OpenFOAM/OpenFOAM-v1906/wmake  yes  yes  often
-------------------------------------------------------------------------------


OpenFOAM env variables in LD_LIBRARY_PATH :
-------------------------------------------------------------------------------
EnvironmentVariable   FileOrDirectory                          Valid Path Crit
-------------------------------------------------------------------------------
$FOAM_LIBBIN          ...06/platforms/linux64GccDPInt32Opt/lib  yes  yes  yes
$FOAM_SITE_LIBBIN     ...06/platforms/linux64GccDPInt32Opt/lib  no        no
$FOAM_USER_LIBBIN     ...06/platforms/linux64GccDPInt32Opt/lib  no        no
$FOAM_EXT_LIBBIN      ...v1906/platforms/linux64GccDPInt32/lib  yes  yes  maybe
$MPI_ARCH_PATH        --------- env variable not set ---------            yes
-------------------------------------------------------------------------------


Software Components
-------------------------------------------------------------------------------
Software  Version    Location  
-------------------------------------------------------------------------------
flex      2.5.37     /bin/flex                                                 
wmake     1906       ...zha518/ny81/zzha518/OpenFOAM/OpenFOAM-v1906/wmake/wmake
gcc       4.8.5      /bin/gcc                                                  
g++       4.8.5      /bin/g++                                                  
gzip      1.5        /bin/gzip                                                 
tar       1.26       /bin/tar                                                  
icoFoam   *** not installed ***
          CRITICAL ERROR

-------------------------------------------------------------------------------


Summary
-------------------------------------------------------------------------------
Base configuration ok.
The foam installation contains 1 critical error(s).

Review the output for warning messages and consult
the installation guide for troubleshooting.

Done
I am not sure what causes the issue and what should i be doing?

Thank you very much in advance!!!!

Last edited by wyldckat; August 25, 2019 at 09:11. Reason: Added [CODE][/CODE] markers
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Old   August 25, 2019, 09:12
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Quick question: In that page you provided, it gives a link to the Build page: https://www.openfoam.com/code/build-guide.php - did you follow the instructions given on that page?
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Old   August 26, 2019, 23:37
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zhenhai zhang
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Quote:
Originally Posted by wyldckat View Post
Quick question: In that page you provided, it gives a link to the Build page: https://www.openfoam.com/code/build-guide.php - did you follow the instructions given on that page?

Hello Bruno
Thanks for replying.
Yes i follow everything on the build page and when i try the command 'foamSystemCheck' it says the following:


Code:
bash: foamSystemCheck: command not found...
And when i try to source the bashrc file, the following is shown:


Code:
bash: mpicc: command not found...
No completion added for /home/zzha518/ny81/zzha518/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/bin
But, after this i can use the 'foam' command to go to the OpenFoam installation directory.


So i am not sure what is the cause of the problem

Thank you very much !!!

Last edited by wyldckat; August 27, 2019 at 18:52. Reason: Added [CODE][/CODE] markers
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Old   August 27, 2019, 19:01
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Quick answers:
  1. The command foamSystemCheck will only work after you activated the OpenFOAM shell environment, namely after you source the "bashrc" file.
  2. The message:
    Code:
    bash: mpicc: command not found...
    is because there is no Open-MPI ready to be used... check if you have any module with Open-MPI ready to be used by running:
    Code:
    module avail
    I expect it's something like "openmpi-x86_64" or "mpi/openmpi-x86_64" that is available in your system. If you do have it, you can load it by running, for example:
    Code:
    module load mpi/openmpi-x86_64
    then source OpenFOAM's "bashrc" file once again.
  3. The message:
    Code:
    No completion added for ...
    is being shown because OpenFOAM-v9106 hasn't been compiled yet.
  4. Then to compile OpenFOAM-v1906, use the following commands:
    Code:
    ./Allwmake -j 4 -log=log.make
    where 4 is the number of cores to use to build/compile OpenFOAM.
    The output is sent to the file "log.make" which you can check its contents on another terminal, e.g. by running:
    Code:
    tail -F log.make
    This log file is critical for diagnosing any compilation problems.
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Old   August 27, 2019, 21:25
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zhenhai zhang
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Hello Bruno



Thank you for your reply !



When i tried your suggestion, i found out that my university's cluster does not have 'openmpi-x86_64' available, so i loaded a one of existing openmpi which is 'openmpi/1.10.7-mlx'



then i tried to compile the openFOAM with ./Allwmake and i get the following warning:



Code:
/home/zzha518/ny81/zzha518/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Finalize'
/home/zzha518/ny81/zzha518/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_op_sum'
/home/zzha518/ny81/zzha518/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Buffer_attach'
/home/zzha518/ny81/zzha518/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Group_free'
collect2: error: ld returned 1 exit status
make[3]: *** [/home/zzha518/ny81/zzha518/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/bin/rhoPorousSimpleFoam] Error 1
make[2]: *** [rhoPorousSimpleFoam] Error 2
make[1]: *** [rhoSimpleFoam] Error 2
make: *** [compressible] Error 2

By the looks of error message, i am not sure if it is to do with the openmpi that i did not use the right one or something else i am not doing correctly. So the Openmpis that is available in the cluster is as follows:



Code:
openmpi/1.10.3-gcc4-mlx
openmpi/1.10.3-gcc4-mlx-cuda75
openmpi/1.10.3-gcc4-mlx-verbs
openmpi/1.10.3-gcc4-mlx-verbs-cuda75
openmpi/1.10.3-gcc5
openmpi/1.10.3-gcc5-mlx
openmpi/1.10.7-1.mlx
openmpi/1.10.7-intel
openmpi/1.10.7-mlx(default)
openmpi/3.1.4-mlx
opennmt-py/0.7.0

And i am so sorry if i am asking very obvious questions, but i have zero experience in doing jobs in cluster previously.


Thank your very much for your patience!
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Old   August 28, 2019, 19:21
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Quick answer: The commands you should execute are as follows:
Code:
module load openmpi/1.10.7-mlx
source $HOME/OpenFOAM/OpenFOAM-v1906/etc/bashrc
(I'm assuming the path on the second line works in your installation, but if not, adjust accordingly)
Then check what error messages you get. If you only get the error about "no completion added", then Open-MPI should be ready to be used with OpenFOAM.

If so far so good, then run:
Code:
foam
./Allwmake -j 4 -log=log.make

However, if sourcing OpenFOAM's "etc/bashrc" file gave the error about mpicc or some other error, then run:
Code:
echo $MPI_ARCH_PATH
ls -l $MPI_ARCH_PATH
ls -l $MPI_ARCH_PATH/include
and tell us what it gives you.
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Old   August 29, 2019, 04:28
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zhenhai zhang
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Hi Bruno

Thanks for replying!

When i load the openmpi and source the bashrc, there was nothing happening in the command window so i waited for a hour or two and found out there was still nothing. and i can not type any command either except ctrl+C to terminate the process.

Code:
[zzha518@monarch-login1 ~]$ source /home/zzha518/ny81/zzha518/OpenFOAM/OpenFOAM-v1906/etc/bashrc

I am not sure if it is suppose to take that long to source the bashrc or anything has gone wrong again?


But the following is the what i get when i call the $MPI_ARCH_PATH
Code:
[zzha518@monarch-login1 ~]$ echo $MPI_ARCH_PATH
/usr/local/openmpi/1.10.7-mlx
Code:
[zzha518@monarch-login1 ~]$ ls -l $MPI_ARCH_PATH
total 13
drwxr-xr-x 2 chines monashuniversity 70 Mar 14  2018 bin
drwxr-xr-x 2 chines monashuniversity  7 Mar 14  2018 etc
drwxr-xr-x 6 chines monashuniversity 25 Mar 14  2018 include
drwxr-xr-x 4 chines monashuniversity 83 Dec  3  2018 lib
drwxr-xr-x 4 chines monashuniversity 84 Nov 30  2018 lib2
drwxr-xr-x 5 chines monashuniversity  5 Mar 14  2018 share
Code:
[zzha518@monarch-login1 ~]$ ls -l $MPI_ARCH_PATH/include
total 97
-rw-r--r-- 1 chines monashuniversity    255 Mar 14  2018 mpi-ext.h
-rw-r--r-- 1 chines monashuniversity   2712 Mar 14  2018 mpif-config.h
-rw-r--r-- 1 chines monashuniversity  10974 Mar 14  2018 mpif-constants.h
-rw-r--r-- 1 chines monashuniversity   1954 Mar 14  2018 mpif-externals.h
-rw-r--r-- 1 chines monashuniversity    188 Mar 14  2018 mpif-ext.h
-rw-r--r-- 1 chines monashuniversity   2715 Mar 14  2018 mpif.h
-rw-r--r-- 1 chines monashuniversity   7740 Mar 14  2018 mpif-handles.h
-rw-r--r-- 1 chines monashuniversity   2122 Mar 14  2018 mpif-io-constants.h
-rw-r--r-- 1 chines monashuniversity   1207 Mar 14  2018 mpif-io-handles.h
-rw-r--r-- 1 chines monashuniversity   2955 Mar 14  2018 mpif-sentinels.h
-rw-r--r-- 1 chines monashuniversity   1152 Mar 14  2018 mpif-sizeof.h
-rw-r--r-- 1 chines monashuniversity 166835 Mar 14  2018 mpi.h
-rw-r--r-- 1 chines monashuniversity  16055 Mar 14  2018 mpi_portable_platform.h
drwxr-xr-x 2 chines monashuniversity      4 Mar 14  2018 mpp
drwxr-xr-x 3 chines monashuniversity      3 Mar 14  2018 openmpi
drwxr-xr-x 3 chines monashuniversity      4 Mar 14  2018 openshmem
-rw-r--r-- 1 chines monashuniversity  19913 Mar 14  2018 pshmem.h
-rw-r--r-- 1 chines monashuniversity  13158 Mar 14  2018 pshmemx.h
-rw-r--r-- 1 chines monashuniversity   1384 Mar 14  2018 shmem-compat.h
-rw-r--r-- 1 chines monashuniversity   1692 Mar 14  2018 shmem.fh
-rw-r--r-- 1 chines monashuniversity  21648 Mar 14  2018 shmem.h
-rw-r--r-- 1 chines monashuniversity  12515 Mar 14  2018 shmemx.h
drwxr-xr-x 3 chines monashuniversity     23 Mar 14  2018 vampirtrace

Regards
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Old   September 1, 2019, 20:41
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zhenhai zhang
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Hi Bruno



It seems that it was the server to have a technical issue from my last post to not respond.


And this is what i get when i run the process again when the cluster is normal again.

So when i try to load the openmpi-1.10.7 i give the following message:

Code:
[zzha518@monarch-login2 ~]$ module load openmpi/1.10.7-1.mlx
    DO NOT USE THIS MODULE> IT IS FOR TESTING ONLY
[zzha518@monarch-login2 ~]$ source /home/zzha518/ny81/zzha518/OpenFOAM/OpenFOAM-v1906/etc/bashrc
bash: mpicc: command not found...
bash: mpicc: command not found...

So i changed to another openmpi (openmpi/1.10.3-gcc5). then i source the bashrc and get the following:

Code:
[zzha518@monarch-login2 ~]$ module load openmpi/1.10.3-gcc5
[zzha518@monarch-login2 ~]$ source /home/zzha518/ny81/zzha518/OpenFOAM/OpenFOAM-v1906/etc/bashrc
mpicc: error while loading shared libraries: libslurm.so.30: cannot open shared object file: No such file or directory
mpicc: error while loading shared libraries: libslurm.so.30: cannot open shared object file: No such file or directory
mpicc: error while loading shared libraries: libslurm.so.30: cannot open shared object file: No such file or directory

Any suggesting on where should i proceed next?

Thank you very much!!



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