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wyldckat October 31, 2010 09:15

Greetings Venkatraman,
Quote:

Originally Posted by maruthamuthu_venkatraman (Post 281482)
There are no plans to update the RHEL version in near future . So I need to live with this system for the time being .

I know the feeling...

Quote:

Originally Posted by maruthamuthu_venkatraman (Post 281482)
Some told me that there is a possibility to copy the compiled gcc, gmp and mpfr ? and paste it on ThirdPaty-1.7.x/platforms/LinuxGcc location to solve this issue.

Disclaimer: I haven't tested this yet... But here are few guidelines:
  1. Download the Third-party package from CentFOAM, chapter Manual install.
  2. Unpack it in a temporary folder.
  3. Read and implement point 3 from this page on your OpenFOAM installation: Automated scripts for building gcc 4.4.x and 4.5.x for using with OpenFOAM 1.7 series
  4. When you've finished implementing point 3, start a new terminal and activate (i.e., source) OpenFOAM's environment. For example:
    Code:

    . $HOME/OpenFOAM/OpenFOAM-1.7.x/etc/bashrc
  5. Now this command will tell you where, for example, gcc-4.4.4 should be installed:
    Code:

    echo $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/gcc-4.4.4
  6. Go to the package you downloaded and extracted from CentFOAM, find that same folder and move its contents to the folder given in the previous command.
  7. Now run:
    Code:

    which gcc
    gcc -v

    It should show you where the visible gcc is placed and which version it is.
You could also try copying gcc 4.3.3 from the ThirdParty binary packages for OpenFOAM 1.6.

Now, this may or may not work, since there could be incompatibilities between the recent gcc builds and the old glibc version in RHEL 3/4.
And keep in mind that the gcc-4.4.4 version from CentFOAM is x86_64 only, so if your RHEL is x86, you will have to try gcc 4.3.3 from OpenFOAM 1.6. Run this if you don't know which one you have:
Code:

uname -m
Best regards,
Bruno

maruthamuthu_venkatraman November 2, 2010 12:49

Thanks for your hints....I will try and let you know.

johny November 8, 2010 10:56

Hi Bruno, I'm back after my short holidays...I got my linux updated Linux 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux Red Hat Enterprise Linux Client release 5.4 (Tikanga) and somehow managed:) to upgrade my compiler to gcc -v Using built-in specs. Target: x86_64-unknown-linux-gnu Configured with: ../configure --prefix=/opt/gcc --program-suffix=444-real --with-ppl --with-cloog --with-mpfr=/opt/gcc --with-gmp --enable-languages=c,c++,fortran --enable-shared --enable-multiarch --enable-linker-build-id --enable-threads=posix --enable-checking --with-system-zlib --with-pkgversion=tygier Thread model: posix gcc version 4.4.4 (tygier) Now when I the ./Allwmake in the OpenFOAM-1.7.1 directory I'm getting a lot of messages like(just one of them pasted below) SOURCE=topoChangerFvMesh/topoChangerFvMesh.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-40 -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/finiteVolume/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/dynamicFvMesh/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/dynamicMesh/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/meshTools/lnInclude -IlnInclude -I. -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/OpenFOAM/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/topoChangerFvMesh.o /bin/sh: g++: command not found and eventually terminates with errors... I guess this means that it cannot find the g++ compiler... When I pick one of the above messages and replace g++ with g++444 which is my new compiler it runs.... Do you have any idea where can I alternate something so that this g++ is replaced by g++444....I hope to get it solved by that.... Looking forward to your reply. Thanks
Quote:

Originally Posted by johny (Post 281203)
Thanks Bruno for the support....I think I got to ask the administrator for an urgent update !!!


johny November 8, 2010 11:01

Hi Bruno, I'm back after my short holidays...I got my linux updated Linux 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux Red Hat Enterprise Linux Client release 5.4 (Tikanga) and somehow managed to upgrade my compiler to gcc -v Using built-in specs. Target: x86_64-unknown-linux-gnu Configured with: ../configure --prefix=/opt/gcc --program-suffix=444-real --with-ppl --with-cloog --with-mpfr=/opt/gcc --with-gmp --enable-languages=c,c++,fortran --enable-shared --enable-multiarch --enable-linker-build-id --enable-threads=posix --enable-checking --with-system-zlib --with-pkgversion=tygier Thread model: posix gcc version 4.4.4 (tygier) Now when I do ./Allwmake in the OpenFOAM-1.7.1 directory I'm getting a lot of messages like(just one of them pasted below) SOURCE=topoChangerFvMesh/topoChangerFvMesh.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-40 -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/finiteVolume/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/dynamicFvMesh/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/dynamicMesh/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/meshTools/lnInclude -IlnInclude -I. -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/OpenFOAM/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/topoChangerFvMesh.o /bin/sh: g++: command not found and eventually terminates with errors... I guess this means that it cannot find the g++ compiler... When I pick one of the above messages and replace g++ with g++444 which is my new compiler it runs.... Do you have any idea where can I alternate something so that this g++ is replaced by g++444....I hope to get it solved by that.... Looking forward to your reply. Thanks
Quote:

Originally Posted by johny (Post 282634)
Hi Bruno, I'm back after my short holidays...I got my linux updated Linux 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux Red Hat Enterprise Linux Client release 5.4 (Tikanga) and somehow managed:) to upgrade my compiler to gcc -v Using built-in specs. Target: x86_64-unknown-linux-gnu Configured with: ../configure --prefix=/opt/gcc --program-suffix=444-real --with-ppl --with-cloog --with-mpfr=/opt/gcc --with-gmp --enable-languages=c,c++,fortran --enable-shared --enable-multiarch --enable-linker-build-id --enable-threads=posix --enable-checking --with-system-zlib --with-pkgversion=tygier Thread model: posix gcc version 4.4.4 (tygier) Now when I the ./Allwmake in the OpenFOAM-1.7.1 directory I'm getting a lot of messages like(just one of them pasted below) SOURCE=topoChangerFvMesh/topoChangerFvMesh.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-40 -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/finiteVolume/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/dynamicFvMesh/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/dynamicMesh/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/meshTools/lnInclude -IlnInclude -I. -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/OpenFOAM/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/topoChangerFvMesh.o /bin/sh: g++: command not found and eventually terminates with errors... I guess this means that it cannot find the g++ compiler... When I pick one of the above messages and replace g++ with g++444 which is my new compiler it runs.... Do you have any idea where can I alternate something so that this g++ is replaced by g++444....I hope to get it solved by that.... Looking forward to your reply. Thanks


wyldckat November 8, 2010 11:09

Hi Jonhy,

Wow, your posts got somehow super condensed :confused: Suggestion: use Advanced mode for editing your posts!

And that update to gcc 4.4.4, you should share how you got it done ;)
As for your problem with g++444, see this explanation: OpenFOAM install on RHEL 5.5 post #2

Best regards,
Bruno

johny November 8, 2010 11:12

Just noticed that the command "which gcc" gives /usr/bin/gcc (where gcc lies) against /opt/gcc/bin/ where g++444 lies......
Quote:

Originally Posted by johny (Post 282636)
Hi Bruno, I'm back after my short holidays...I got my linux updated Linux 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux Red Hat Enterprise Linux Client release 5.4 (Tikanga) and somehow managed to upgrade my compiler to gcc -v Using built-in specs. Target: x86_64-unknown-linux-gnu Configured with: ../configure --prefix=/opt/gcc --program-suffix=444-real --with-ppl --with-cloog --with-mpfr=/opt/gcc --with-gmp --enable-languages=c,c++,fortran --enable-shared --enable-multiarch --enable-linker-build-id --enable-threads=posix --enable-checking --with-system-zlib --with-pkgversion=tygier Thread model: posix gcc version 4.4.4 (tygier) Now when I do ./Allwmake in the OpenFOAM-1.7.1 directory I'm getting a lot of messages like(just one of them pasted below) SOURCE=topoChangerFvMesh/topoChangerFvMesh.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-40 -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/finiteVolume/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/dynamicFvMesh/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/dynamicMesh/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/meshTools/lnInclude -IlnInclude -I. -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/OpenFOAM/lnInclude -I/home/joseph/OpenFOAM/OpenFOAM-1.7.1/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/topoChangerFvMesh.o /bin/sh: g++: command not found and eventually terminates with errors... I guess this means that it cannot find the g++ compiler... When I pick one of the above messages and replace g++ with g++444 which is my new compiler it runs.... Do you have any idea where can I alternate something so that this g++ is replaced by g++444....I hope to get it solved by that.... Looking forward to your reply. Thanks


maruthamuthu_venkatraman November 9, 2010 05:36

OpenFOAM1.7.x installation on RHEL 4.0 cluster
 
1 Attachment(s)
Hello Bruno,
I followed your guidelines as u mentioned in last reply. I will explain you in detail so that if I miss anything you may able to guide me better.

1. I downloaded the OpenFoam1.7.x and extracted and renamed in home/OpenFoam/OpenFOAM-1.7.x

2. Then the Thirdparty1.7.0 was also downloaded and renamed as Thirdparty-1.7.x

3. As you said , the compiler of the system was changed in to OPENFOAM in the sttings.csh and the versions are changed into 4.4.4 for gcc.

4. Since i use X86_64 arcitecture in the OpenFoam cshrc file I changed the commands in gcc and g++ to gcc44 and g++44

5. I sourced the openFoam cshrc file

6. In the downloaded CENTFOAM third party i found a directory platforms/linux64/gcc4.4.4 . But this platforms directory was not there in the Thirdparty1.7.x stuff that i downloaded from the git repository. So i copied the directory 'platforms' completely and pasted it in the ThirdParty 1.7.x.

7. gcc -version gives GCC-4.4.4 and it is pointing the right location.

8. Then I executed ./Allwmake > log.allwmake


But there are many errors displayed in the terminal window. However they are not shown in log files. I hereby attach the log output file for your reference. If you can have a look at it it will be useful to me.

Thanks and Regards

wyldckat November 9, 2010 18:32

Greetings Venkatraman,

Please run again but like this:
Code:

./Allwmake > log.allwmake  2>&1
This way the errors will also be outputed into the log file.

All I can figure out is that something very weird is happening, due to binaries being built as "OpenFOAM.out" :confused:

So, my guess is that it's either flex or binutils that is missing...

Best regards,
Bruno

maruthamuthu_venkatraman November 10, 2010 05:19

1 Attachment(s)
Dear Bruno,
I hereby attached the Log files with error messages. I checked Flex version it says flex 2.5.4 and Bison 1.875c .

If you can tell me what are the packages that are missing for RHEL 4.0 X86_64 , to install OF 1.7.x then it will be useful. I had an Appt with LINUX admin tomorrow, If you cna tell me either by today or tomorrow it wil be useful.

Thanks and Regards

wyldckat November 10, 2010 07:11

Hi Venkatraman,

Bad news, the gcc version you've got doesn't work :(

Try following this tutorial and you will see what I mean: Compiling a simple C++ program

You better ask your system's administrator to build you an updated gcc, either 4.4.4/4.4.5 or 4.5.1, including the latest binutils. Apparently the version built the CentOS 5.x is too much in the future for possible compatibility with RHEL/CentOS 4.x.

If your system's administrator can't build an up-to-date gcc+binutils, try installing CentOS 4.x in a virtual machine, build gcc+binutils (and maybe OpenFOAM as well) and then copy the resulting build to your RHEL 4 machine.

Another way to check if gcc is working is to run this:
Code:

cd $WM_DIR/src
make

This should build wmake's assistant tools: wmkdep and dirToString. Without these, you won't be able to build OpenFOAM.

Best regards and good luck!
Bruno

maruthamuthu_venkatraman November 12, 2010 09:02

Dear Bruno,
You are right ! The gcc4.4.4 provided by CentFOAM is not compatible to build OpenFOAM1.7.x on RHEL 4.0 . This was not possible with my experience.

Now Iam building OpenFOAM on CENTOS-5.5 on a seperate workstation. I followed the steps for manual installation provided in CentFOAM website. OF1.7.0 was installed without any flaws.

Then I downloaded OF1.7.x and changed the settings for gcc compiler from system to OpenFoam and version 4.4.4 in settings.sh. Path is also set using alias command for .bashrc file .

For the thirdparty directory , i copied the existing Thirdparty-1.7.0 (from centFOAM)and just renamed the director y as ThirdParty- 1.7.x. I got only one error as of now. Could you tell me what is the problem.

make:*** [/opt/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libscotchDecomp.so] Error 1


Thanks

wyldckat November 12, 2010 11:27

Hi Muthu,

Quote:

Originally Posted by maruthamuthu_venkatraman (Post 283243)
make:*** [/opt/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libscotchDecomp.so] Error 1

:eek: I'm gonna need to know more than that ;)

Run Allwmake like this:
Code:

./Allwmake > make.log 2>&1
tar -czf make.log.tar.gz make.log

Then please post the compressed log file; otherwise I can only make wild guesses, such as:
  • libscotch didn't build properly...
  • OpenMPI wasn't properly built or something...

Best regards,
Bruno

johny November 14, 2010 13:44

Hi Bruno,
Sorry that I couldn't share my experience. I was just away for a week on official reasons. Anyway it seems that my installation really didn't work well(even after trying to get the compiler linking issue in order) and there were a lot of compiler incompatibilites and dependencies error that my colleague decided to get a fresh installation.

Could you please shed some light in the following 2 issues regarding bc's

1)How can I mention the inlet velocity in OpenFOAM when the boundary under consideration is a curved surface of a cylinder and flow(inlet velocity) should be tangential(or lets at an angle to the normal) to this surface and away from the axis of this cylindrical surface. Basically this cylindrical surface is an inlet to a cabin and air is drove into the cabin with a fan alligned to the axis of the surface(cylindrical)

2)Here again is about the inlet velocity bc. In the wind tunnel simulation flow enters the tunnel through the inlet normal to the inlet surface. But if I want to mention the velocity at an angle to the to inlet surface, how can I do it.

I would greatly appreciate a reply and looking forward to it...

Cheers !!!


Quote:

Originally Posted by wyldckat (Post 282638)
Hi Jonhy,

Wow, your posts got somehow super condensed :confused: Suggestion: use Advanced mode for editing your posts!

And that update to gcc 4.4.4, you should share how you got it done ;)
As for your problem with g++444, see this explanation: OpenFOAM install on RHEL 5.5 post #2

Best regards,
Bruno


wyldckat November 14, 2010 17:13

Hi Johny,
Quote:

Originally Posted by johny (Post 283409)
Anyway it seems that my installation really didn't work well(even after trying to get the compiler linking issue in order) and there were a lot of compiler incompatibilites and dependencies error that my colleague decided to get a fresh installation.

A very wise decision :)

Quote:

Originally Posted by johny (Post 283409)
Could you please shed some light in the following 2 issues regarding bc's
(...)
I would greatly appreciate a reply and looking forward to it...

:( I'm so sorry, but on those types of questions, I don't know much (--> here <-- is more about what I do and don't know ;)). And I believe it's best that you ask those questions on the dedicated section of this forum: OpenFOAM Running / Solving / CFD
Or like many people do, ask on the main OpenFOAM forum.

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

OK, the rest of this post I will use for my report on my experiences this weekend with CentOS:
  • I've installed in 4 virtual machines the CentOS i386 versions 3.3, 3.9, 4.0 and 4.8. The first 3 were downloaded from CentOS's vault.
  • In all of them I was successful in building OpenFOAM 1.7.1, without much effort.
  • Each machine was configured with 20GB of disk, 1.6GB of RAM, 4 cores and always installed CentOS in Workstation mode, since it already comes with development tools pre-installed, so I didn't need to mess around with the package manager nor yum :)
  • All of these CentOSes come with flex 2.5.4, which was more than enough for building OpenFOAM 1.7.1.
  • All of them come with gcc series 3.x.x, which was more than enough for building make, binutils and gcc 4.4.4. I haven't tried gcc 4.5.1, but it should well enough as well :)
  • In CentOS 3.x versions, I had to build a more recent GNU make, but I've just included it in my build-gcc scripts (see here).
  • Other than this, I didn't need to build a new flex, nor need to build any other more recent tools!
So, it's pretty simple:
  1. follow the instructions in www.openfoam.com for building either OpenFOAM 1.7.1 or 1.7.x (although I haven't tried the git versions that come with these CentOSes)...
  2. BUT just before you run Allwmake, follow the instructions on this blog post: Automated scripts for building gcc 4.4.x and 4.5.x for using with OpenFOAM 1.7 series
  3. After this, keep following the original instructions for building OpenFOAM and you should have it all working after a few hours.
I didn't try to build ParaView in these CentOSes, since that's a whole other ball game ;)

As for that previous issue reported on this thread, namely post #19, it probably happened solely because there was a folder path in the environment variable LD_LIBRARY_PATH that carried a "rogue" library... which could be the pre-built ParaView 3.8.0 available only. In such a scenario, it's necessary to neutralize that path... and such explanation will have to wait for another time, because I don't want to over-post ;)

So, to conclude:
  • If you do have an RHEL 5.x, try CentFOAM first.
  • For those people who need to build OpenFOAM in an old RHEL (version < 5.0), have no root access to that machine, you can try at first following these instructions above. If they don't work, install CentOS of the same version as your RHEL, in a Virtual Machine or on a real machine, and be sure to install the Workstation version (question appears during installation). Then follow these instructions again. When done, pack the whole OpenFOAM folder and take it to your RHEL machine and modify OpenFOAM-1.7.1/etc/bashrc if necessary, to adapt the folder paths.
Good luck! Best regards,
Bruno

maruthamuthu_venkatraman November 15, 2010 03:19

1 Attachment(s)
Dear Bruno,
I hereby attach the compressed log file to see the details of comiplation. Actually I can able to run foamInstallationTest and it says all crictical systema and basic configurations are Ok. I also ran some testcases and the results are okey.

But still I want to make it sure that this Error comes from where ? Does it has any influence later ?

Thanks

wyldckat November 15, 2010 09:45

Dear Muthu,

The only error there is in the log file is for libscotchDecomp, just as you previously posted about. Sorry about that, I didn't understand before that this was the only error. The solution is quite simple: run Allwmake again and the error will be solved :)

The error is one of the issues I've recently reported to OpenCFD's bug tracking system:
Quote:

Originally Posted by http://www.openfoam.com/mantisbt/view.php?id=79
when doing a completely clean build of OpenFOAM, libscotch and libptscotch don't get copied to the target folders, because when doing a completely new build, the folders haven't been created by wmake yet. Therefore, some libraries and applications aren't built on the first run. A second run goes well, because the target folders already exist.

Best regards,
Bruno

maruthamuthu_venkatraman November 15, 2010 09:56

Thanks a lot Bruno! I will do it as you said. This clears my mind :-) .

flowris April 27, 2011 10:00

1 Attachment(s)
Hello,

I installed 1.7.x on a computer cluster and I am trying to do some parallel runs with the cavity case. All goes well, when I type my commands manually:
Code:

blockMesh
decomposePar
mpirun -np 8 icoFoam -parallel
reconstructPar

If I want to user different nodes, I qsub a file named run.sge which contains this:
Code:

#!/bin/sh 
#  request Bourne shell as shell for job
#$ -S /bin/sh
#$ -N cavity
#$ -m beas
#$ -M joris.mattheijssens@rma.ac.be
# Specify a MPI job on N processors
#$ -pe orte 8
#$ -cwd
# -j y standard error redirected in the same file as the standard output
#$ -o log -j y
#$ -v MPI_BUFFER_SIZE=200000000
. ~/OpenFOAM/OpenFOAM-1.7.x/etc/bashrc

rm machines
cat $PE_HOSTFILE | awk '{ print $1 " slots=" $2 }' > machines

decomposePar
mpirun --hostfile machines -np $NSLOTS --byslot icoFoam -parallel > log
reconstructPar
rm core*

I have a similar error message to msuho in #19 in my log file (see log.txt)

Can anybody tell me what the problem is?

gschaider April 27, 2011 11:11

Quote:

Originally Posted by flowris (Post 305294)
Hello,

I installed 1.7.x on a computer cluster and I am trying to do some parallel runs with the cavity case. All goes well, when I type my commands manually:
Code:

blockMesh
decomposePar
mpirun -np 8 icoFoam -parallel
reconstructPar

If I want to user different nodes, I qsub a file named run.sge which contains this:
Code:

#!/bin/sh 
#  request Bourne shell as shell for job
#$ -S /bin/sh
#$ -N cavity
#$ -m beas
#$ -M joris.mattheijssens@rma.ac.be
# Specify a MPI job on N processors
#$ -pe orte 8
#$ -cwd
# -j y standard error redirected in the same file as the standard output
#$ -o log -j y
#$ -v MPI_BUFFER_SIZE=200000000
. ~/OpenFOAM/OpenFOAM-1.7.x/etc/bashrc

rm machines
cat $PE_HOSTFILE | awk '{ print $1 " slots=" $2 }' > machines

decomposePar
mpirun --hostfile machines -np $NSLOTS --byslot icoFoam -parallel > log
reconstructPar
rm core*

I have a similar error message to msuho in #19 in my log file (see log.txt)

Can anybody tell me what the problem is?

Problem ist that the libstdc++ that it finds on the cluster is WAY too old. Let the script output

echo $LD_LIBRARY_PATH

and

ldd interFoam

(or whatever your solver is). Compare the outputs. See what is there. Is your cluster and your workstation the same RedHat-release? Which gcc did you use for compilation (maybe you'll have to install the compiler - or only the standard libraries that come with it - on the cluster too)

Bernhard

flowris April 28, 2011 03:26

Thank you.

I am not sure my libstdc++ is too old, since I used gcc-4.5.1.

What I do not understand is the following : Both simulations I describe above were tried on the same cluster, with CentOS release 5.4 (Final). When I type the commands one by one, it works, but when I use the run.sge, the troubles come.

I added the lines to run.sge. echo $LD_LIBRARY_PATH gives
Code:

/home/jmatthei/OpenFOAM/ThirdParty-1.7.x/platforms/linux64Gcc/paraview-3.8.0/lib/paraview-3.8:/home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1:/home/jmatthei/OpenFOAM/ThirdParty-1.7.x/platforms/linux64Gcc/openmpi-1.4.1/lib:/home/jmatthei/OpenFOAM/jmatthei-1.7.x/lib/linux64GccDPOpt:/home/jmatthei/OpenFOAM/site/1.7.x/lib/linux64GccDPOpt:/home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt:/home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/dummy:/opt/gridengine/lib/lx26-amd64:/usr/lib64/openmpi/1.4.1-gcc/lib:/share/apps/intel/lib/intel64:/share/apps/intel/ipp/em64t/sharedlib:/share/apps/intel/mkl/lib/em64t
ldd icoFoam gives an empty output, or when I type it directly in the terminal it gives
ldd: ./icoFoam: No such file or directory

So I went into OpenFOAM/OpenFOAM-1.7.x/applications/bin/linux64GccDPOpt and then typed ldd icoFoam, which gave

Code:

    libfiniteVolume.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libfiniteVolume.so (0x00002ae2b8f96000)
    libOpenFOAM.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libOpenFOAM.so (0x00002ae2b9fd1000)
    libdl.so.2 => /lib64/libdl.so.2 (0x0000003db7200000)
    libstdc++.so.6 => /share/apps/gcc-4.5.1/lib64/libstdc++.so.6 (0x00002ae2ba660000)
    libm.so.6 => /lib64/libm.so.6 (0x0000003db6e00000)
    libgcc_s.so.1 => /share/apps/gcc-4.5.1/lib64/libgcc_s.so.1 (0x00002ae2ba966000)
    libc.so.6 => /lib64/libc.so.6 (0x0000003db6a00000)
    libPstream.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1/libPstream.so (0x00002ae2bab7b000)
    libtriSurface.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libtriSurface.so (0x00002ae2bad85000)
    libmeshTools.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libmeshTools.so (0x00002ae2baffd000)
    libz.so.1 => /usr/lib64/libz.so.1 (0x0000003db7a00000)
    /lib64/ld-linux-x86-64.so.2 (0x0000003db6600000)
    libmpi.so.0 => /home/jmatthei/OpenFOAM/ThirdParty-1.7.x/platforms/linux64Gcc/openmpi-1.4.1/lib/libmpi.so.0 (0x00002ae2bb457000)
    libdecompositionMethods.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libdecompositionMethods.so (0x00002ae2bb6f9000)
    liblagrangian.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/liblagrangian.so (0x00002ae2bb919000)
    libopen-rte.so.0 => /home/jmatthei/OpenFOAM/ThirdParty-1.7.x/platforms/linux64Gcc/openmpi-1.4.1/lib/libopen-rte.so.0 (0x00002ae2bbb37000)
    libopen-pal.so.0 => /home/jmatthei/OpenFOAM/ThirdParty-1.7.x/platforms/linux64Gcc/openmpi-1.4.1/lib/libopen-pal.so.0 (0x00002ae2bbd86000)
    libnsl.so.1 => /lib64/libnsl.so.1 (0x0000003db9a00000)
    libutil.so.1 => /lib64/libutil.so.1 (0x0000003dc3400000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003db7600000)
    libscotchDecomp.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libscotchDecomp.so (0x00002ae2bbfff000)
    libmetisDecomp.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libmetisDecomp.so (0x00002ae2bc20c000)
    libparMetisDecomp.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1/libparMetisDecomp.so (0x00002ae2bc41b000)
    libscotch.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libscotch.so (0x00002ae2bc631000)
    libscotcherrexit.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libscotcherrexit.so (0x00002ae2bc891000)
    libmetis.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libmetis.so (0x00002ae2bca92000)
    libGKlib.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libGKlib.so (0x00002ae2bcce5000)
    libmetis-parmetis.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1/libmetis-parmetis.so (0x00002ae2bcf00000)
    libparmetis.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1/libparmetis.so (0x00002ae2bd14a000)

I am not sure about what this means, but I think the problem is not in libstdc++, since for both the library is in /share/apps/gcc-4.5.1/lib64/libstdc++.so.6.

Don't you think the problem is somewhere in the run.sge file?

flowris April 28, 2011 04:44

OK, we solved the problem by adding a line to the run.sge to source our gcc-4.5.1.

gschaider April 28, 2011 08:08

Quote:

Originally Posted by flowris (Post 305381)
Thank you.

I am not sure my libstdc++ is too old, since I used gcc-4.5.1.

That's the one you built it with. The binaries produced need a corresponding dynamic library and that is not present on your cluster (or it can't find it)

Quote:

Originally Posted by flowris (Post 305381)
What I do not understand is the following : Both simulations I describe above were tried on the same cluster, with CentOS release 5.4 (Final). When I type the commands one by one, it works, but when I use the run.sge, the troubles come.

I added the lines to run.sge. echo $LD_LIBRARY_PATH gives
Code:

/home/jmatthei/OpenFOAM/ThirdParty-1.7.x/platforms/linux64Gcc/paraview-3.8.0/lib/paraview-3.8:/home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1:/home/jmatthei/OpenFOAM/ThirdParty-1.7.x/platforms/linux64Gcc/openmpi-1.4.1/lib:/home/jmatthei/OpenFOAM/jmatthei-1.7.x/lib/linux64GccDPOpt:/home/jmatthei/OpenFOAM/site/1.7.x/lib/linux64GccDPOpt:/home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt:/home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/dummy:/opt/gridengine/lib/lx26-amd64:/usr/lib64/openmpi/1.4.1-gcc/lib:/share/apps/intel/lib/intel64:/share/apps/intel/ipp/em64t/sharedlib:/share/apps/intel/mkl/lib/em64t
ldd icoFoam gives an empty output, or when I type it directly in the terminal it gives
ldd: ./icoFoam: No such file or directory

So I went into OpenFOAM/OpenFOAM-1.7.x/applications/bin/linux64GccDPOpt and then typed ldd icoFoam, which gave

Code:

    libfiniteVolume.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libfiniteVolume.so (0x00002ae2b8f96000)
    libOpenFOAM.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libOpenFOAM.so (0x00002ae2b9fd1000)
    libdl.so.2 => /lib64/libdl.so.2 (0x0000003db7200000)
    libstdc++.so.6 => /share/apps/gcc-4.5.1/lib64/libstdc++.so.6 (0x00002ae2ba660000)
    libm.so.6 => /lib64/libm.so.6 (0x0000003db6e00000)
    libgcc_s.so.1 => /share/apps/gcc-4.5.1/lib64/libgcc_s.so.1 (0x00002ae2ba966000)
    libc.so.6 => /lib64/libc.so.6 (0x0000003db6a00000)
    libPstream.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1/libPstream.so (0x00002ae2bab7b000)
    libtriSurface.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libtriSurface.so (0x00002ae2bad85000)
    libmeshTools.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libmeshTools.so (0x00002ae2baffd000)
    libz.so.1 => /usr/lib64/libz.so.1 (0x0000003db7a00000)
    /lib64/ld-linux-x86-64.so.2 (0x0000003db6600000)
    libmpi.so.0 => /home/jmatthei/OpenFOAM/ThirdParty-1.7.x/platforms/linux64Gcc/openmpi-1.4.1/lib/libmpi.so.0 (0x00002ae2bb457000)
    libdecompositionMethods.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libdecompositionMethods.so (0x00002ae2bb6f9000)
    liblagrangian.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/liblagrangian.so (0x00002ae2bb919000)
    libopen-rte.so.0 => /home/jmatthei/OpenFOAM/ThirdParty-1.7.x/platforms/linux64Gcc/openmpi-1.4.1/lib/libopen-rte.so.0 (0x00002ae2bbb37000)
    libopen-pal.so.0 => /home/jmatthei/OpenFOAM/ThirdParty-1.7.x/platforms/linux64Gcc/openmpi-1.4.1/lib/libopen-pal.so.0 (0x00002ae2bbd86000)
    libnsl.so.1 => /lib64/libnsl.so.1 (0x0000003db9a00000)
    libutil.so.1 => /lib64/libutil.so.1 (0x0000003dc3400000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003db7600000)
    libscotchDecomp.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libscotchDecomp.so (0x00002ae2bbfff000)
    libmetisDecomp.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libmetisDecomp.so (0x00002ae2bc20c000)
    libparMetisDecomp.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1/libparMetisDecomp.so (0x00002ae2bc41b000)
    libscotch.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libscotch.so (0x00002ae2bc631000)
    libscotcherrexit.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libscotcherrexit.so (0x00002ae2bc891000)
    libmetis.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libmetis.so (0x00002ae2bca92000)
    libGKlib.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/libGKlib.so (0x00002ae2bcce5000)
    libmetis-parmetis.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1/libmetis-parmetis.so (0x00002ae2bcf00000)
    libparmetis.so => /home/jmatthei/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1/libparmetis.so (0x00002ae2bd14a000)

I am not sure about what this means, but I think the problem is not in libstdc++, since for both the library is in /share/apps/gcc-4.5.1/lib64/libstdc++.so.6.

Don't you think the problem is somewhere in the run.sge file?

No idea and frankly I don't have the patience to work out other peoples DLL-mixups. Log into the cluster (first by ssh then with qlogin) start your script by hand and see when it stops working. Let your script output all environment variables with "export" and see what is the difference. Good luck

makaveli_lcf October 25, 2011 09:03

Hi! I need to build 1.7.x on the RHEL-5. But it seems that now only 2.0.x 1.6.x-dev are left of the centFOAM repository. How could I install 1.7.x?

makaveli_lcf October 25, 2011 09:14

For 1.6-ext installation got following error:

Code:

[smmplogin OpenFOAM$][smmplogin OpenFOAM$]./centFOAM.py --OF16
All packages will be downloaded to this folder
 and extracted to /SAS/home/alexanderv/centFOAM/
Press enter to continue
installing OpenFOAM-1.6-ext to /SAS/home/alexanderv/centFOAM//OpenFOAM/OpenFOAM-1.6-ext
Folder exists
Already downloaded OpenFOAM-1.6-ext.tar.gz,skipping
Unpacking OpenFOAM-1.6-ext.tar.gz, might take a minut or two
Replacing foamInstall=/home/44792/centFoam/$WM_PROJECT with foamInstall=/SAS/home/alexanderv/centFOAM//$WM_PROJECT in file/SAS/home/alexanderv/centFOAM//OpenFOAM/OpenFOAM-1.6-ext/etc/bashrc
Traceback (most recent call last):
  File "./centFOAM.py", line 235, in ?
    main()   
  File "./centFOAM.py", line 230, in main
    installOpenFOAM(options.path, "1.6-ext", "OF16")
  File "./centFOAM.py", line 157, in installOpenFOAM
    replaceInLine(bashFile,"foamInstall=/home/44792/centFoam/$WM_PROJECT","foamInstall="+path+"/$WM_PROJECT")
  File "./centFOAM.py", line 20, in replaceInLine
    for line in fileinput.FileInput(file,inplace=1):
  File "/usr/lib64/python2.4/fileinput.py", line 231, in next
    line = self.readline()
  File "/usr/lib64/python2.4/fileinput.py", line 300, in readline
    os.rename(self._filename, self._backupfilename)
OSError: [Errno 2] No such file or directory


makaveli_lcf October 25, 2011 09:41

Found a problem:
OF20 extracts everything to $HOME/centFOAM/OpenFOAM-2.0.x
OF16 to $HOME/centFOAM/OpenFOAM/OpenFOAM-1.6-ext

Rebecca513 October 28, 2011 10:50

Dear Bruno,

I am using CentOS Linux release 6.0 (Final), and trying to install OpenFOAM.

I tried to install centFOAM, though it is supposed to be used for 5.x. Anyway, the installation didn't give any error, but when I tried to use icoFoam, it says that the command is not found. I guess the installation failed after all.

I wonder if you could give me some suggestions as how I should proceed to install OpenFOAM on my computer.

Thank you so much!

Best,

Hang

wyldckat October 28, 2011 14:04

Greetings Hang,

I haven't tried CentOS 6.0, but by what I just saw in distrowatch, you should have absolutely no problems in installing OpenFOAM 2.0.1 simply by following the instructions provided on the official OpenFOAM website... Well, at least after you manage to install all of the right system packages ;)

Anyway, CentOS 6.0 has gcc 4.4.4 ready to be used, without any need for further compiling of another Gcc version. So that's a nice head start that you already have over CentOS 5.x.

So, let's try this:
  1. Run Allwmake on OpenFOAM's 2.0.1 or 2.0.x main folder like this:
    Code:

    ./Allwmake > make.log 2>&1
  2. Open the file "make.log" with a text editor and replace any sensitive folder paths and usernames. Save and close the file.
  3. Then pack the file into a nice tarball:
    Code:

    tar -czf make.log.tar.gz make.log
  4. Then attach the newly created file "make.log.tar.gz" to your next post.
This way I can see what exactly is going on wrong.

Best regards,
Bruno

Rebecca513 October 28, 2011 16:35

1 Attachment(s)
Hi Bruno,

Thank you for the quick reply and step-by-step instruction. That is really what I need since I am quite new to both linux and OF.

The error given by the make.log is quite short, actually it is

./Allwmake: line 4: wmakeCheckPwd: command not found
Error: Current directory is not $WM_PROJECT_DIR
The environment variables are inconsistent with the installation.
Check the OpenFOAM entries in your dot-files and source them.

Now I am thinking maybe because I installed it as root, but not under the directory of root. But it seems that it is installed in the directory I want.

foamInstall=/home/hangdeng/centFOAM/$WM_PROJECT

I attached the bashrc file. If you could take a look.

Thank you so much for your help. I really appreciate it.

wyldckat October 29, 2011 05:01

Hi Hang,

OK, let's try changing the following lines:
  • foamCompiler=ThirdParty - change to system
  • export WM_COMPILER=Gcc45 - change to Gcc44
Now:
  1. Start a new terminal as root.
  2. Check what Gcc version the following command gives you:
    Code:

    gcc -v
    Hopefully it states that it's 4.4.4 or similar.
  3. Check if your environment has the right variables initiated:
    Code:

    export
    See if you can see the variables that were described in the previous "bashrc" file.
    1. If the variables aren't there, run:
      Code:

      source /home/hangdeng/centFOAM/OpenFOAM/OpenFOAM-2.0.x/etc/bashrc
    2. Check again if the environment is up and running.
  4. OK, now try running the command I wrote about in the previous post.
And that should do it. At least to figure out what else is missing :)

Best regards,
Bruno

Rebecca513 October 30, 2011 19:04

1 Attachment(s)
Hello Bruno,

Thank you for the reply. And sorry for the late response. Failed to come to the office as it was snowing quite a bit yesterday.

I did as you posted,
After running gcc -v
It gives

gcc version 4.4.4 20100726 (Red Hat 4.4.4-13) (GCC)

Also, I attached the make.log.

BTW, I was trying to play with the meshing packages in centFOAM since OF is not working, seems that other than engrid, gmsh and netgen are not working either. I am not sure whether it is caused by similar reasons. Anyway, I think I should let you know, in case such information is some sort of indicator to find out the problem.

Thank you!

wyldckat October 31, 2011 07:16

Hi Hang,

Mmmm, you're getting a particular problem to CentFOAM's presets. I advise you to put CentFOAM on the side for now and try things with the original OpenFOAM: http://www.openfoam.com/download/source.php

If you want to stick to CentFOAM, then edit the file "Allwmake" that is on the "ThirdParty-2.0.x" folder and comment out the lines that state something like this:
Code:

        # Infiniband support
        if [ -d /usr/local/ofed -a -d /usr/local/ofed/lib64 ]
        then
            configOpt="$configOpt --with-openib=/usr/local/ofed"
            configOpt="$configOpt --with-openib-libdir=/usr/local/ofed/lib64"
        fi

Then try again.

Best regards,
Bruno

Rebecca513 October 31, 2011 14:46

Hello Bruno,

Thank you!

The lines have already been commented out actually.

So I tried to compile OF following the link you posted.

I got OF work, at least some simple cases.

But I couldn't get ParaView compiled. I have already installed very new versions of QT and cmake, still, everytime I run 'makeParaView', it gives:

*** Error: cannot find qmake either at $QMAKE_PATH or in current $PATH

Do you have any idea why that happens.

Thank you!

Best,

Hang

Rebecca513 October 31, 2011 14:57

Sorry Bruno,

I take what I said back. It turned out that OF is not working. Also, it always gives command not found.

I have no idea why it works at first, then nothing...It is so frustrating...

wyldckat October 31, 2011 15:01

Hi Hang,

About your second post:
  • The make.log file might help me help you!?
  • Run:
    Code:

    echo $WM_PROJECT_DIR
    to see which version of OpenFOAM your current terminal is set to use.

OK, as for your post before that: where exactly did you install Qt and CMake? Were they installed by using the package manager that comes with CentOS?

If you installed with the package manager, then try finding out what's the complete name of the installed executable. For example, if you type a part of a name of an application in the terminal command line and then press the Tab key once or twice, it should try to auto-complete the full name or show you what alternatives exist. For example, typing:
Code:

qmake
then hit the Tab key twice, you should show you something like:
Code:

qmake-4.6
qmake-4.7

then you type what's missing and you're set to go.

For qmake, this works; but for cmake, it gets a bit tricky...

OK, but when you find out what's the whole name of qmake, run makeParaView similarly to this:
Code:

./makeParaView -qmake  `which qmake-4.6`
If cmake goes by another name, then a symbolic link is usually the quickest way to make things work:
Code:

ln -s `cmake-2.8.3` $FOAM_APPBIN/cmake
If you need to build ParaView with a custom Qt version, here's a blog post of mine that might help you: Building ParaView 3.10.1 with custom Qt 4.6.4

Best regards,
Bruno

Rebecca513 October 31, 2011 17:12

Hi Bruno,

1
I remembered that before I ran makeParaView, OF worked, after makeParaView, OF failed. I know it is reckless, I deleted everything and did the compilation from the very beginning again, hoping that I could at least have a working OF. Speak of stupidity....Anyway, I will send you the new make.log as soon as I get it.

[hangdeng@cee-5dpjzq1 OpenFOAM]$ echo $WM_PROJECT_DIR
/home/hangdeng/OpenFOAM/OpenFOAM-2.0.1

2
qmake I have on the computer is qmake-qt4.6, I guess that means I need to build ParaView with custom qt?

echo $WM_THIRD_PARTY_DIR gives back empty...

and (I guess that is why)

[hangdeng@cee-5dpjzq1 ThirdParty-2.0.1]$ ./makeParaView -qmake 'which qmake-qt4'
./makeParaView: line 36: wmakeCheckPwd: command not found
Error: Current directory is not $WM_THIRD_PARTY_DIR
The environment variables are inconsistent with the installation.
Check the OpenFOAM entries in your dot-files and source them.

Also,

[hangdeng@cee-5dpjzq1 OpenFOAM]$ ln -s `cmake-2.8.4` $FOAM_APPBIN/cmake
bash: cmake-2.8.4: command not found
ln: creating symbolic link `./cmake': File exists

Rebecca513 October 31, 2011 19:55

Hi Bruno,

I just finished compiling OF, and I checked It is working. I attached the make.log anyway.

But somehow, last time, after I tried to run the makeParaView (or install qmake & cmake), it failed.

So, now I am gonna play on the safe side in terms of compiling paraView. I wonder if the information in the previous post showed any of the problem. Or I should go ahead and try what you posted for compiling paraview with custom QT?

Thank you so much for your patient help!

Best,

Hang

wyldckat November 1, 2011 03:23

Hi Hang,

Well, I don't see any "make.log.tar.gz" attached on your latest 2 posts ;)

You might want to read this blog post of mine: Advanced tips for working with the OpenFOAM shell environment - it explains a bit how the OpenFOAM shell environment works, which might help you understand the problem you were having.

As for compiling ParaView, it's up to you to choose the best option. I don't have time in the next few days to test installing OpenFOAM on virtual machines with CentOS 6.0, so I won't be able to write a lengthy blog post explaining step by step on how to do so :(

Best regards,
Bruno

Rebecca513 November 1, 2011 09:11

Hi Bruno,

Thank you for your kind help. It has been really a big help.

I will keep trying the options available.

I really appreciate your help!

Best,

Hang

linnemann November 1, 2011 15:22

Quote:

Originally Posted by makaveli_lcf (Post 329366)
For 1.6-ext installation got following error:

Code:

[smmplogin OpenFOAM$][smmplogin OpenFOAM$]./centFOAM.py --OF16
All packages will be downloaded to this folder
 and extracted to /SAS/home/alexanderv/centFOAM/
Press enter to continue
installing OpenFOAM-1.6-ext to /SAS/home/alexanderv/centFOAM//OpenFOAM/OpenFOAM-1.6-ext
Folder exists
Already downloaded OpenFOAM-1.6-ext.tar.gz,skipping
Unpacking OpenFOAM-1.6-ext.tar.gz, might take a minut or two
Replacing foamInstall=/home/44792/centFoam/$WM_PROJECT with foamInstall=/SAS/home/alexanderv/centFOAM//$WM_PROJECT in file/SAS/home/alexanderv/centFOAM//OpenFOAM/OpenFOAM-1.6-ext/etc/bashrc
Traceback (most recent call last):
  File "./centFOAM.py", line 235, in ?
    main()   
  File "./centFOAM.py", line 230, in main
    installOpenFOAM(options.path, "1.6-ext", "OF16")
  File "./centFOAM.py", line 157, in installOpenFOAM
    replaceInLine(bashFile,"foamInstall=/home/44792/centFoam/$WM_PROJECT","foamInstall="+path+"/$WM_PROJECT")
  File "./centFOAM.py", line 20, in replaceInLine
    for line in fileinput.FileInput(file,inplace=1):
  File "/usr/lib64/python2.4/fileinput.py", line 231, in next
    line = self.readline()
  File "/usr/lib64/python2.4/fileinput.py", line 300, in readline
    os.rename(self._filename, self._backupfilename)
OSError: [Errno 2] No such file or directory


Hi this has now been fixed.

As to the centFOAM and RHEL 6.x I will have versions up sometime.
There already are some files you can download manually for 6.x which can be found here.

It should be fairly easy to get it running you just have make the right entries in your .bashrc. I've tried experimenting with rpms instead of tar.gz but I think I will go back to the tar.gz approach as I have more freedom to manipulate which stuff goes into the packages so they can be run as standalone packages.

Please do not use the centFOAM.py script for 6.x. I will have an automatic detection of which version you are running, sometime in the future, when I have time.

The reason I'm not focusing on 6.x yet is that our cluster and machines aren't using 6.x but 5.x.

I can although tell you that making OF compile on 6.x is a breeze since GCC is fairly up to date.


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