[amuzeshi]

Dear all,

Although I have access to solids4Foam, but, when I use an hpc server, I can not install it there, because I hava no sudo permission. Therefore I have to use icoFsiElasticNonLinULSolidFoam, because foam-extend-3.1 is installed on the server (And yes, again I can not install fsi toolkit, because I'm not sudoer). So, there are two questions:

1- Is there a solution for a non-sudo user on a hpc server to use solids4Foam?
2- To validate the solver for an elastic cylinder fsi problem, I want to start from the problem of flow around rigid cylinder, using the same solver as in fsi problem. In solids4Foam, it is easy to turn-off fsi and turn-on only flow simulatoin. Assuming we use icoFsiElasticNonLinULSolidFoam, is turning off fsi in couplingProperties dictionary gives the same result? [As I investigated the code, this solver indeed solves the solid region an it is not possible to turn it off... ] ?

[wyldckat]

Quick answer: You can build a more recent version of foam-extend and solids4Foam as a normal user.
Either way, you don't need sudo/root/admin permissions to install solids4Foam, it's mostly designed to be built as a normal user.

However, the HPC system administrators might not like that people compile a complete installation of foam-extend in the user's own account... but if they don't like it, then ask them nicely to install the foam-extend version that you need.
On the login node, you should have access to all compilation tools needed to build foam-extend, if they have foam-extend 3.1 installed there.

[amuzeshi]

Originally Posted by wyldckat

Quick answer: You can build a more recent version of foam-extend and solids4Foam as a normal user.
Either way, you don't need sudo/root/admin permissions to install solids4Foam, it's mostly designed to be built as a normal user.

However, the HPC system administrators might not like that people compile a complete installation of foam-extend in the user's own account... but if they don't like it, then ask them nicely to install the foam-extend version that you need.
On the login node, you should have access to all compilation tools needed to build foam-extend, if they have foam-extend 3.1 installed there.

Thank you. After I tried to compile foam-extend-4.0 on an HPC server using this help, I received a lot of errors of the kind I mentioned in the following. As I checked, environment variables like FOAM_RUN etc are known, but blockMesh, icoFoam, etc are not known to the terminal.

-ldynamicMesh     -lmeshTools     -llagrangian -lfoam -ldl   -lrt -lm -o /home/user/foam/foam-extend-4.0/applications/bin/linux64GccDPOpt/autoRefineMesh
/usr/bin/ld: cannot find -lfoam
collect2: ld returned 1 exit status
make[3]: *** [/home/user/foam/foam-extend-4.0/applications/bin/linux64GccDPOpt/autoRefineMesh] Error 1
make[2]: *** [autoRefineMesh] Error 2
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-200 -I/home/user/foam/foam-extend-4.0/src/meshTools/lnInclude -IlnInclude -I. -I/home/user/foam/foam-extend-4.0/src/foam/lnInclude -I/home/user/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/surfaceInvertNormal.o -L/home/user/foam/foam-extend-4.0/lib/linux64GccDPOpt \

[amuzeshi]

Originally Posted by wyldckat

Quick answer: You can build a more recent version of foam-extend and solids4Foam as a normal user.
Either way, you don't need sudo/root/admin permissions to install solids4Foam, it's mostly designed to be built as a normal user.

However, the HPC system administrators might not like that people compile a complete installation of foam-extend in the user's own account... but if they don't like it, then ask them nicely to install the foam-extend version that you need.
On the login node, you should have access to all compilation tools needed to build foam-extend, if they have foam-extend 3.1 installed there.

Doing these preparations that are documented in OpenfoamWiki, requires me to be a sudoer. However I mounted my own account on the hpc server to a directory in my laptop using "sshfs". Then I tried to go thru preparation steps and compilation using my local compiler. Untill now, It has returned no error, but it is very very slow !

[wyldckat]

Originally Posted by amuzeshi

However I mounted my own account on the hpc server to a directory in my laptop using "sshfs". Then I tried to go thru preparation steps and compilation using my local compiler. Untill now, It has returned no error, but it is very very slow !

Quick answer: You were almost there... you don't need to use sshfs, you can clone your laptop installation of foam-extend to your account on the HPC server.

1. Deactivate the "sshfs" connection.
2. You can follow the instructions given here: https://openfoamwiki.net/index.php/I..._3.0_and_newer - to remove the intermediate files that were used to build foam-extend in your machine.
3. Then you can use the following commands in your laptop to package the installation:
   

   foam
   cd ..
   tar -czf foam-extend-4.0_full.tar.gz foam-extend-4.0

4. Then transfer the file "foam-extend-4.0_full.tar.gz" into your home folder at the HPC server.
5. Then you can unpack it with this command:
   

   tar -xzf foam-extend-4.0_full.tar.gz

   Make sure you run it in a way that it will unpack into the correct location, for example, place this file at "~/foam/" and then the command from within that folder.

[amuzeshi]

Originally Posted by wyldckat

Quick answer: You were almost there... you don't need to use sshfs, you can clone your laptop installation of foam-extend to your account on the HPC server....

Great!
I went thru the steps that you've mentioned;
1- While Executing 'fe40' as alias, makes environment variables like 'run' or '$FOAM_TUTORIALS' known, but it returns:

mpicc: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/maneshian.sharif/foam/foam-extend-4.0/ThirdParty/packages/openmpi-1.8.8/platforms/linux64GccDPOpt/lib/libopen-pal.so.6)

2- Executing 'icoFoam' returns:

icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /home/ali/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblagrangian.so)
icoFoam: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/ali/foam/foam-extend-4.0/ThirdParty/packages/openmpi-1.8.8/platforms/linux64GccDPOpt/lib/libopen-rte.so.7)

[wyldckat]

Quick question: Wait, then how did you make it work via sshfs? Did you add any additional paths via sshfs?

[amuzeshi]

Originally Posted by wyldckat

Quick question: Wait, then how did you make it work via sshfs? Did you add any additional paths via sshfs?

Note: For clarification, I use '~' as my laptop home directory and '$HOME' as my HPC account home directory.

1- My own method:

• a-
  

  sshfs ali@<address> ~/ali/server/

• b- In ~/ali/home/.bashrc file, I add:
  

  source ~/ali/server/foam/foam-extend-4.0/etc/bashrc

• c- It takes too ( ) long for the compilation to complete.

2- Following your method step-by-step, ends up with the errors I've mentioned in the previous post. Additionally, icoFoam, for example, is known to my terminal (typing 'icoF', then pressing 'TAB' completes the word as 'icoFoam'). But solids4Foam is not known !

• It should be mentioned that I added the following to $/HOME/ali/.bashrc file:
  

  source $HOME/foam/foam-extend-4.0/etc/bashrc