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[OpenFOAM.org] OpenFOAM 4.1 on cluster with Scientific Linux

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Old   December 21, 2016, 12:23
Default OpenFOAM 4.1 on cluster with Scientific Linux
  #1
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Dear all,

I am having a hard time installing OpenFOAM 4.1 on a cluster where I have no admin rights.

I was mainly using the information here starting at #5:
http://openfoamwiki.net/index.php/In...HEL#CentOS_6.5

Everything worked fine, I think, till step #7. When I type "uname -m" I am getting: "x86_64"
So I was using the commands
Code:
module load openmpi-x86_64 || export PATH=$PATH:/usr/lib64/openmpi/bin
which gave me the error "ModuleCmd_Load.c(204):ERROR:105: Unable to locate a modulefile for 'openmpi-x86_64'"

Code:
"source $HOME/OpenFOAM/OpenFOAM-4.1/etc/bashrc WM_LABEL_SIZE=64 WM_COMPILER_TYPE=ThirdParty FOAMY_HEX_MESH=yes"
and
Code:
echo "alias of41='module load openmpi-x86_64; source \$HOME/OpenFOAM/OpenFOAM-4.1/etc/bashrc $FOAM_SETTINGS'" >> $HOME/.bashrc
which also gives me the error:
"oduleCmd_Load.c(204):ERROR:105: Unable to locate a modulefile for 'openmpi-x86_64'"

So, according to this thread's post #8 and #9:
OpenFoam installation on CentOs 6.5 without root access

I used "module avail" and got the following results (only showing information regarding openmpi here):
Code:
 /etc/modulefiles/parallel --------------------------------------------------------------------------------
cuda/5.5               cuda/6.5(default)      openmpi/1.5.4          openmpi/1.8.2(default) openmpi/1.8.2intel
cuda/6.0               cuda/7.5               openmpi/1.6.5          openmpi/1.8.2cuda
Therefore, I changed "openmpi-x86_64" in the commands above to "openmpi/1.8.2".
After ". .bashrc" and "of41" there is no error msg anymore.

After that everything works fine, as far as I can tell, but in #14, the compilation stops at 2%. The last lines of the log file:
Code:
[  2%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/compiler/importer.cc.o
[  2%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/compiler/parser.cc.o
Linking C shared library ../../../../lib/libvtklibxml2-pv5.0.so
[  2%] Built target vtklibxml2
Linking CXX executable ../../../../bin/protoc
[  2%] Built target protoc_compiler
make: *** [all] Error 2
Anyways, I do not really need paraview on the cluster, so I tried to continue with step #15.
Running Allwmake in $WM_PROJECT_DIR unfortunately gives me the following error (changed the name of the user to "..."):

Code:
Compiling enabled on 4 cores
make: Nothing to be done for `all'.

========================================
Start ThirdParty Allwmake
========================================

========================================
Build MPI libraries if required

+ cd openmpi-1.10.2
/home/.../OpenFOAM/ThirdParty-4.1/Allwmake: line 78: cd: openmpi-1.10.2: No such file or directory
+ exit 1

Well, he is looking for openmpi-1.10.2, I guess, but there is no folder for openmpi in the Third Party folder. So, I checked another installation of OpenFOAM 1.6, which was installed by a colleague of mine years ago. In the Third Party folder for version 1.6 I can find an openmpi-1.3.3 folder FWIW.

Let me know what information I should provide additionally. Looking forward for your help.
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Old   December 22, 2016, 06:34
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OK, good news: It is compiling at the moment for some minutes w/o errors yet. I am not really sure why exactly but I changed the following line in the bashrc.
Code:
WM_MPLIB=SYSTEMOPENMPI
Then I ran the adjusted (openmpi/1.8.2) commands in step #7 (https://openfoamwiki.net/index.php/I...CentOS_SL_RHEL)
This time I used the command for 32 Bit instead of 64 Bit as before.
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Old   September 11, 2017, 21:55
Default so your running 32 bit now
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forgive me, but I would think that would be a real hindrance to the quality of the simulations. I have constructed my own cluster with Xenserver and Scientific Linux 7 and I hit a very similar issue.

My plan was to go through the SL7 install directions and make sure that I had actually run the commands correctly. It's something that is probably going to take me days, because I am far from fast at this. Mostly because I am still learning how Linux OS system works. So I am expecting there will be a learning curve there.

In-case you have a better solution, that you have come up with in the mean time, I just wanted to checkin and ask. Anything that was helpful or other tips for the rest of us SL users?

What about the new version. Looks like OF foundation is saying that we should use Docker?! Don't know about you but I am really hesitant to volunteer to learn another software. I am sure that docker is really cool, but I personally have enough on my plate, and would like to avoid this if it is going to be another rabbit hole.
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Old   December 31, 2017, 12:14
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Greetings to all!

I'm really late on this, but:
Quote:
Originally Posted by LeeRuns View Post
forgive me, but I would think that would be a real hindrance to the quality of the simulations. I have constructed my own cluster with Xenserver and Scientific Linux 7 and I hit a very similar issue.
Without more details on which instructions you've followed, and without any error messages, it's not possible to give any specific answers.
If anything, you are looking for installation instructions to which version of OpenFOAM on SL7?


Quote:
Originally Posted by LeeRuns View Post
What about the new version. Looks like OF foundation is saying that we should use Docker?! Don't know about you but I am really hesitant to volunteer to learn another software. I am sure that docker is really cool, but I personally have enough on my plate, and would like to avoid this if it is going to be another rabbit hole.
The Docker builds are just provided as a somewhat convenient way of providing a single installation package for any Linux Distribution.

The reason why they are not providing more instructions for other distributions is rather simple: no one nor any company is sponsoring that work, namely to support native builds of OpenFOAM on other Linux Distributions.

The option of building from source code always exists and it should be a lot easier nowadays.

Beyond this, if you need specific installation instructions, you can always ask here on the forum for them. I usually try to make as many available as possible at https://openfoamwiki.net/index.php/Installation - but as time grows short, I've had to keep the instructions to a minimum, mostly to the versions I use and the ones that people ask for.

Best regards,
Bruno
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