[linnemann]

Hi Manoj


As already posted above

Note that from June 2010 Paraview will be a separate program from OpenFOAM and thus paraFoam will no longer work. This was a decision I've made since I feel the performance from the parallel reader found here is superior to the one in OpenFOAM. It also means that you can use Paraview without OpenFOAM and it allows me to keep Paraview more up to date. To use Paraview with the new reader just create an empty file in your case folder "touch casename.foam" and open this file using Paraview.

[linnemann]

@alberto

csh settings should now be generic when installing from centFOAM.py script.


also gmsh-2.5.0 with OCC support and paraview-3.10.1 is now avaliable.

[anmartin]

hello,
First at all, many thanks for sharing your work.
I have installed OF20 and paraview without any problem, but when i try to run in paralel I obtanin the following error.
I will be very grateful if someone can help me.
Best regards


[cluster.div:10512] mca: base: component_find: unable to open /home/anmartin/OpenFOAM/ThirdParty-2.0.x/platforms/linux64Gcc45/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
librdmacm: couldn't read ABI version.
librdmacm: assuming: 4
libibverbs: Fatal: couldn't read uverbs ABI version.
CMA: unable to open /dev/infiniband/rdma_cm
libibverbs: Fatal: couldn't read uverbs ABI version.
--------------------------------------------------------------------------
[[60751,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: cluster.div
Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
[cluster.div:10513] mca: base: component_find: unable to open /home/anmartin/OpenFOAM/ThirdParty-2.0.x/platforms/linux64Gcc45/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
[cluster.div:10514] mca: base: component_find: unable to open /home/anmartin/OpenFOAM/ThirdParty-2.0.x/platforms/linux64Gcc45/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
[cluster.div:10515] mca: base: component_find: unable to open /home/anmartin/OpenFOAM/ThirdParty-2.0.x/platforms/linux64Gcc45/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
librdmacm: couldn't read ABI version.
librdmacm: assuming: 4
libibverbs: Fatal: couldn't read uverbs ABI version.
librdmacm: couldn't read ABI version.
librdmacm: couldn't read ABI version.
librdmacm: assuming: 4
CMA: unable to open /dev/infiniband/rdma_cm
librdmacm: assuming: 4
libibverbs: Fatal: couldn't read uverbs ABI version.
libibverbs: Fatal: couldn't read uverbs ABI version.
CMA: unable to open /dev/infiniband/rdma_cm
CMA: unable to open /dev/infiniband/rdma_cm
libibverbs: Fatal: couldn't read uverbs ABI version.
libibverbs: Fatal: couldn't read uverbs ABI version.
libibverbs: Fatal: couldn't read uverbs ABI version.
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.0.x |
| \\ / A nd | Web: www.OpenFOAM.com |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.0.x
Exec : interDyMFoam -parallel
Date : Oct 02 2011
Time : 18:41:12
Host : cluster.div
PID : 10512
Case : /home/anmartin/foam/Slosh_II/Oval_II
nProcs : 4
Slaves :
3
(
cluster.div.10513
cluster.div.10514
cluster.div.10515
)
Pstream initialized with:
floatTransfer : 0
nProcsSimpleSum : 0
commsType : nonBlocking
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

[linnemann]

Ahh yes

This is because I built openmpi with infiniband support which we have in our cluster.

try running it like this

mpirun --mca btl ^openib --mca btl_tcp_if_include eth0 --hostfile hostfile -n 2 simpleFoam -parallel

This disables infiniband but I do not know if it will run.

If it doesn't I will make a version without infiniband.

[xisto]

Hello linnemann

I'm trying to install openFoam 2.0.x in rocks 5.3 (centOs 5.6) but when I tried to run:

python centFOAM.py -p /opt/OpenFOAM --OF20

I got the folowing error:

All packages will be downloaded to this folder
 and extracted to /opt/OpenFOAM
Press enter to continue
installing OpenFOAM-2.0.x to /opt/OpenFOAM/OpenFOAM/OpenFOAM-2.0.x
Folder exists
Already downloaded OpenFOAM-2.0.x.tar.gz,skipping
Unpacking OpenFOAM-2.0.x.tar.gz, might take a minut or two
Replacing foamInstall=/opt/software/$WM_PROJECT with foamInstall=/opt/OpenFOAM/$WM_PROJECT in file/opt/OpenFOAM/OpenFOAM/OpenFOAM-2.0.x/etc/bashrc
Traceback (most recent call last):
  File "centFOAM.py", line 234, in ?
    main()
  File "centFOAM.py", line 227, in main
    installOpenFOAM(options.path, "2.0.x", "OF20")
  File "centFOAM.py", line 153, in installOpenFOAM
    replaceInLine(bashFile,"foamInstall=/opt/software/$WM_PROJECT","foamInstall="+path+"/$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
[root@octopus100 centosFOAM]#

I realy dont know what happend because I put the path=/opt/OpenFOAM, and the scrip tries to modify a file that is in opt/OpenFOAM/OpenFOAM/OpenFOAM-2.0.x/etc/bashrc.

Thanks for your help, and great work

Regards,

Carlos

[linnemann]

Hi

Ive just installed a fresh version of Centos in VB.

As you can see from this line

installing OpenFOAM-2.0.x to /opt/OpenFOAM/OpenFOAM/OpenFOAM-2.0.x

You have a double OpenFOAM directory which will just add to confusion.

The error in the script was that it I forgot to add "OpenFOAM" to the path so that this subdir would be created automatically. And also the bash file path should be changed accordingly.

So the correct way to run the script would be

python centFOAM.py -p /opt --OF20

Then you will have OF installed in

/opt/OpenFOAM/OpenFOAM-2.0.x and ThirdParty in /opt/OpenFOAM/ThirdParty-2.0.x

It will also work with /opt/OpenFOAM but then you have double OpenFOAM subdirs.

Please download the new one and try again.

Thank you very much for the feedback.

[xisto]

Thanks Linnemann

I actually used the manual installation and it worked.

Great job with the script

Carlos

[jsc]

Hello,

First, thank you for the help already posted, because in many cases solves the problems and if not, it helps identifying it.

I am trying to run OpenFOAM in parallel in several nodes. Each node alone can run the case in parallel without problem when executed with "runParallel" instruction. Also, each node alone can run the case in parallel when executed with the "mpirun" instruction, but in this case before the calculations began it displays the next error. But when I try several nodes it display the same error as in the previous case, for each node and the calculation does not begin (Error displayed at the end of this reply).

The OpenFOAM version is 2.1.x, the system is Red Hat 5.7 and it has not infiniband (as I was told by the person which is in charge of the server) so I tried the solution sugested by Niels but it did not work (Error displayed at the end of this reply).

Originally Posted by linnemann

Ahh yes

This is because I built openmpi with infiniband support which we have in our cluster.

try running it like this

mpirun --mca btl ^openib --mca btl_tcp_if_include eth0 --hostfile hostfile -n 2 simpleFoam -parallel

This disables infiniband but I do not know if it will run.

If it doesn't I will make a version without infiniband.

I have also found other sugestion by Niels but I am unsure of the changes required:

Originally Posted by linnemann

Hi Alberto

Ahh yes, our cluster has infiniband so thats why it complains that it cant find it.

one solution is to change the Allwmake script in the Thirdparty folder.

uncomment line 102 where it says --with-openib.

Delete the platforms/linux64Gcc45/openmpi-1.5.3 folder and run ./Allwmake again.

This should then compile without infiniband.

The other solution that you could try beforehand is to run mpi as described at the very bottom on this page http://pkg-ofed.alioth.debian.org/ho...d-howto-6.html this forces openmpi to use tcp-ip.

I will compile a version without inifiniband and upload if youd like.

The refered line of code it is not at line 102, and it is inside a IF sentence. Should I just uncomment the exact line or the entire IF sentence?

Also, any other suggestion or orientation would be very appreciated.

Thank all of you for your help and time.
José Sánchez


Next, it is paste the error I get at first:

[Jose1@flu motorbikeMPI]$ mpirun --hostfile machines -np 6 simpleFoam -parallel
[flu:26946] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
[flu:26947] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
[flu:26948] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
librdmacm: couldn't read ABI version.
librdmacm: couldn't read ABI version.
librdmacm: assuming: 4
librdmacm: assuming: 4
CMA: unable to get RDMA device list
CMA: unable to get RDMA device list
--------------------------------------------------------------------------
[[37872,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: flu

Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
librdmacm: couldn't read ABI version.
librdmacm: assuming: 4
CMA: unable to get RDMA device list
[nodo19:08126] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_btl_ofud: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08125] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_btl_ofud: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08127] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_btl_ofud: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08126] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08125] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08127] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08125] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08126] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08127] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.1.1                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.1.1-221db2718bbb
Exec   : simpleFoam -parallel
Date   : Apr 22 2013
Time   : 13:48:12
Host   : "flu"
PID    : 26946
[flu:26944] 2 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics
[flu:26944] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

Next it is pasted the error I get with the solution sugested by Niels:

[Jose1@flu motorbikeMPI]$ mpirun --mca btl ^openib --mca btl_tcp_if_include eth0 --hostfile machines -np 6 simpleFoam -parallel
[flu:26989] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
[flu:26990] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
[flu:26991] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08322] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_btl_ofud: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08320] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_btl_ofud: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08321] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_btl_ofud: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08322] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08320] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
[nodo19:08321] mca: base: component_find: unable to open /home/users/OpenFOAM/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_mtl_psm: libpsm_infinipath.so.1: cannot open shared object file: No such file or directory (ignored)
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.1.1                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.1.1-221db2718bbb
Exec   : simpleFoam -parallel
Date   : Apr 22 2013
Time   : 14:06:50
Host   : "flu"
PID    : 26989

[jsc]

Hello again,

I have changed the hostfile from:

Jose1@flu cpu=3
Jose1@nodo19 cpu=3

to:

Jose1@nodo19 cpu=3
Jose1@flu cpu=3

and now it runs. I have to do some checks but it seems to be correct so, Does the order in the hostfile matters? (For me apparently yes)
I think it is important to point that "flu" is the master and "nodo19" is supposed to be the slave.