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[OpenFOAM.org] Problems with installing openfoam 5.0 on HPC Cluster |
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June 5, 2018, 11:03 |
Problems with installing openfoam 5.0 on HPC Cluster
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#1 |
New Member
Jin Zhang
Join Date: May 2018
Location: Germany
Posts: 15
Rep Power: 8 |
Hi Foamers,
I am new to the application of OpenFOAM. I want to OpenFOAM5.0 on HPC cluster. I know that if I want to implement a new turbulence model, I have to install OF on my local user directory on Cluster instead of using the default version. I have found some tutorials about installing OF2.x version on cluster, these are the main procedures: (Gcc, MPI etc. are already installed on cluster) 1) cp /cineca/prod/applications/openfoam/2.3.0-gnu-4.7.2/openmpi--1.6.3--gnu--4.7.2/OF_2.3.0_LOCAL_INSTALL_CINECA_PLX.tar . tar -xf OF_2.3.0_LOCAL_INSTALL_CINECA_PLX.tar rm OF_2.3.0_LOCAL_INSTALL_CINECA_PLX.tar cd OF_2.3.0_LOCAL_INSTALL_CINECA_PLX ls OF_2.3.0_LOCAL_INSTALL_CINECA_PLX.sh PATCHES 2) Execute the script to download, configure and install your local version of OpenFOAM: ./OF_2.3.0_LOCAL_INSTALL_CINECA_PLX.sh The installation dir, in this case, is located in your $HOME space FOAM_INST_DIR=$HOME/OpenFOAM The OpenFOAM environment of the local installation is set in $HOME/OpenFOAM/OpenFOAM-2.3.x/etc/bashrc 3) Load the environment of your local installation module load gnu/4.7.2 module load openmpi/1.6.3--gnu--4.7.2 source $HOME/OpenFOAM/OpenFOAM-2.3.x/etc/bashrc and you will have $WM_PROJECT_VERSION=2.3.x $FOAM_INST_DIR=/plx/userinternal/ispisso0/OpenFOAM $WM_PROJECT_USER_DIR=/plx/userinternal/ispisso0/OpenFOAM/ispisso0-2.3.x Now I can find the tar files in the cluster among which OpenFOAM-5.0 is the default opt version I can use directly: 5-0.tar.gz backup2.zig backup.zip bashrc OpenFOAM-5.0 In addition, these modules are now available on cluster: module load comp/gcc/6.3.0 module load mpi/openmpi/2.1.0/gcc I have some questions: 1) Can I just install OF with this file by copying it to my user directory? 2) there is an isolate bashrc file in the directory. I looked inside the file and found that there's only a change with the WM_COMPILER=Icc. Can I just use this bashrc to configure? 3) Apart from the above procedures, what else should I consider? or Could I just use ./Allwmake to compile? Looking forward to reading your answers! Jin |
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January 11, 2019, 15:56 |
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#2 |
New Member
Jin Zhang
Join Date: May 2018
Location: Germany
Posts: 15
Rep Power: 8 |
Hello Bruno,
I know this is an old thread. But I come across the same problem with Openfoam5.0 installed on the HPC cluster and intelMPI. Listed below is the jobscript what I used. module load mpi/intelmpi/2018.1.163 module load intel-studio-2018 module load comp/gcc/6.3.0 module load comp/cmake/3.7.2 module load lib/scotch/6.3.0 source /home/OpenFOAM/OpenFOAM-5.0/etc/bashrc I can run the simulations previously and there's no error. However, when I rerun the cases and kept all things unchanged, it doesn't work and the error are: –> FOAM FATAL ERROR: Trying to use the dummy Pstream library. This dummy library cannot be used in parallel mode From function static bool Foam:UPstream::init(init &, char **&) in file UPstream.C at line 37. FOAM exiting. I did some checks as you suggested. 1) echo $FOAM_MPI when I typed this command, it shows nothing. And then I source the bashrc file and it shows: Warning in /home/OpenFOAM/OpenFOAM-5.0/etc/config.sh/settings: MPI_ROOT not a valid mpt installation directory or ending in a ‘/’. Please set MPI_ROOT to the mpt installation directory. MPI_ROOT currently set to ’ '. So what can I do now to solve this problem? Thanks in advance! Kind regards, Jin [Moderator note: Moved from Pstream library error in parallel mode ] Last edited by wyldckat; January 12, 2019 at 09:05. Reason: see "Moderator note:" |
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January 12, 2019, 09:45 |
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#3 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,982
Blog Entries: 45
Rep Power: 128 |
Greetings Jin,
I've moved your old post into the "OpenFOAM Installation" sub-forum and then moved your more recent post into the same thread as the old one, so that we can stay on the same topic. From the old post, it seems that you had tried to compile with Icc and Open-MPI. But on the more recent post, you seem to be trying to use Icc and Intel MPI. Furthermore, it is possible that someone changed the Intel software stack in the cluster, so it's possible that you built OpenFOAM with an older version of Intel software than the one you are trying to use now. Either way, first let's find out what you used in the old build. Run the following command: Code:
find $FOAM_LIBBIN/ -type d Code:
/home/ofuser/OpenFOAM/OpenFOAM-5/platforms/linux64GccDPInt32Opt/lib/ /home/ofuser/OpenFOAM/OpenFOAM-5/platforms/linux64GccDPInt32Opt/lib/dummy /home/ofuser/OpenFOAM/OpenFOAM-5/platforms/linux64GccDPInt32Opt/lib/openmpi-system /home/ofuser/OpenFOAM/OpenFOAM-5/platforms/linux64GccDPInt32Opt/lib/paraview-5.4 From there, we can workout if you should be trying to use Intel MPI or Open-MPI. If you did compile with Intel MPI, Intel has changed the installation paths sometime ago and has become a bit of a weird convention... which I haven't double-checked yet as to what should be done with it. So once we figure out which one you used, we can then decide from there. Best regards, Bruno
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January 15, 2019, 08:27 |
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#4 |
New Member
Jin Zhang
Join Date: May 2018
Location: Germany
Posts: 15
Rep Power: 8 |
Hello Bruno,
Thanks so much for your reply. I have done what you suggested and it shows: /home/OpenFOAM/OpenFOAM-5.0/platforms/linux64IccDPInt32Opt/lib /home/OpenFOAM/OpenFOAM-5.0/platforms/linux64IccDPInt32Opt/dummy /home/OpenFOAM/OpenFOAM-5.0/platforms/linux64IccDPInt32Opt/2018.1.163 So I think I actually use the IntelMPI 2018.1.163 which is one of the module that I load. Best regards, Jin |
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January 20, 2019, 16:35 |
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#5 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,982
Blog Entries: 45
Rep Power: 128 |
Quick answer:
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Tags |
cluster, installation, of5.0 |
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