CFD Online Discussion Forums - [swak4Foam] swak4Foam installaton issue on cluster

CFD Online Discussion Forums (https://www.cfd-online.com/Forums/)

- OpenFOAM Community Contributions (https://www.cfd-online.com/Forums/openfoam-community-contributions/)

- - [swak4Foam] swak4Foam installaton issue on cluster (https://www.cfd-online.com/Forums/openfoam-community-contributions/149309-swak4foam-installaton-issue-cluster.html)

swak4Foam installaton issue on cluster

I am trying to install swak4foam on my university cluster
which already has OpenFoam installed.
I set up m4 and bison in my home directory and then run ./Allwmake
but I get errors.

Any advice on how to fix this?

Some excerpts from the log file

Code:

No file 'swakConfiguration'. Python etc won't work. See README for details

Checking swak4Foam-version and generating file

Swak version is 0.3.1

Bison is version 2.7.12-4996

Flex is version 2.5.35 (Minor version: 35)

OpenFOAM-version: Major 2 Minor 3 Patch 0 (-1 == x / 0)

No swak4FoamParsers/foamVersion4swak.H. Generated

wmakeLnInclude: linking include files to simpleFunctionObjects/lnInclude

make: Warning: File `linux64GccDPOpt/options' has modification time 87 s in the future

One instance where error occurs

Code:

/usr/local/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Isend'

/usr/local/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Finalize'

/usr/local/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_op_sum'

/usr/local/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Buffer_attach'

/usr/local/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_size'

/usr/local/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Group_free'

/usr/local/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_rank'

collect2: ld returned 1 exit status

make[1]: *** [/home00/xxxx/OpenFOAM/xxxx-2.3.0/platforms/linux64GccDPOpt/bin/funkySetBoundaryField] Error 1

make[1]: warning:  Clock skew detected.  Your build may be incomplete.

make: *** [funkySetBoundaryField] Error 2

g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/usr/local/OpenFOAM/OpenFOAM-2.3.0/src/cfdTools/lnInclude -I/usr/local/OpenFOAM/OpenFOAM-2.3.0/src/cfdTools/general/lnInclude      -I/usr/local/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude         -I/usr/local/OpenFOAM/OpenFOAM-2.3.0/src/meshTools/lnInclude            -I../../Libraries/swak4FoamParsers/lnInclude/ -IlnInclude -I. -I/usr/local/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/usr/local/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/calcNonUniformOffsetsForMapped.o -L/usr/local/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib \

             -lfiniteVolume -lmeshTools -lOpenFOAM -ldl   -lm -o /home00/xxxx/OpenFOAM/xxxx-2.3.0/platforms/linux64GccDPOpt/bin/calcNonUniformOffsetsForMapped

/usr/bin/ld: warning: libmpi.so.1, needed by /usr/local/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so, not found (try using -rpath or -rpath-link)

I have already tried Unable to use/build swak4Foam in a cluster and/or when module load is used from
https://openfoamwiki.net/index.php/I...e_load_is_used

How do I go about (try using -rpath or -rpath-link)?

Hi canopus

Have you figured it out? I am also trying to install swak4foam in my university's cluster, I will let you know if I success.

Cheers,
Kan

Unfortunately not so far. Trying to get hold of sys admin and running things on desktop for time being!

Greetings to all!

Regarding the time issue:

Code:

make: Warning: File `linux64GccDPOpt/options' has modification time 87 s in the future

You can solve it by running:

Code:

find ./ | xargs touch

which will reset time snapshot to the current date-time.

As for the other problem with the missing "libmpi.so.1", I need specific details on what are the exact steps you need to do in order to load the OpenFOAM shell environment in your system. Namely, what "module load" commands you need to do?

Best regards,
Bruno

Hi Bruno,

Could you please have a look at my bug while installing swak4foam at HPC cluster.

Here is the top of log file while installation:

Code:

This is a clean install

No file 'swakConfiguration'. Python etc won't work. See README for details

Checking swak4Foam-version and generating file

    abort: There is no Mercurial repository here (.hg not found)!

Swak version is 0.3.1

Bison is version 2.4.1

Flex is version 2.5.35 (Minor version: 35)

OpenFOAM-version: Major  Minor  Patch  (-1 == x / )

No swak4FoamParsers/foamVersion4swak.H. Generated

wmakeLnInclude: linking include files to simpleFunctionObjects/lnInclude

And blow is the tail of log file:

Code:

In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(50): error: expected an expression

  #if (FOAM_VERSION4SWAK_MAJOR < 2)

                               ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(66): error: expected an expression

      #if (FOAM_VERSION4SWAK > VERSION_NR2(1,7) && !defined(FOAM_DEV)) || (FOAM_VERSION4SWAK > VERSION_NR2(3,0))

           ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(66): error: expected an expression

      #if (FOAM_VERSION4SWAK > VERSION_NR2(1,7) && !defined(FOAM_DEV)) || (FOAM_VERSION4SWAK > VERSION_NR2(3,0))

                                                                           ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(71): error: expected an expression

  #if !((FOAM_VERSION4SWAK_MAJOR > 1) || (FOAM_VERSION4SWAK_MINOR > 6))

                                 ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(71): error: expected an expression

  #if !((FOAM_VERSION4SWAK_MAJOR > 1) || (FOAM_VERSION4SWAK_MINOR > 6))

                                                                  ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(76): error: expected an expression

  #if defined(FOAM_DEV) || FOAM_VERSION4SWAK_MAJOR>1

                                                  ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(86): error: expected an expression

  #if FOAM_VERSION4SWAK < VERSION_NR(1,7,0) || defined(FOAM_DEV)

      ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(90): error: expected an expression

  #if FOAM_VERSION4SWAK <= VERSION_NR2(2,1) || defined(FOAM_DEV)

      ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(95): error: expected an expression

  #if FOAM_VERSION4SWAK < VERSION_NR(2,1,0) || defined(FOAM_DEV)

      ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(107): error: expected an expression

  #if (FOAM_VERSION4SWAK >= VERSION_NR(2,1,0)) && !defined(FOAM_DEV)

       ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(118): error: expected an expression

  #if FOAM_VERSION4SWAK > VERSION_NR2(2,1)

      ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(181): error: expected an expression

  #if FOAM_VERSION4SWAK < VERSION_NR(1,7,0) || defined(FOAM_DEV)

      ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(185): error: expected an expression

  #if (FOAM_VERSION4SWAK > VERSION_NR2(2,1)) && !defined(FOAM_DEV)

       ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(256): error: expected an expression

  #if FOAM_VERSION4SWAK > VERSION_NR2(2,2) && !defined(FOAM_DEV)

      ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(260): error: expected an expression

  #if FOAM_VERSION4SWAK > VERSION_NR2(2,2) && !defined(FOAM_DEV)

      ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(264): error: expected an expression

  #if FOAM_VERSION4SWAK < VERSION_NR(2,3,0) || defined(FOAM_DEV)

      ^



In file included from helpers/printSwakVersion.C(44):

lnInclude/swak.H(268): error: expected an expression

  #if (FOAM_VERSION4SWAK > VERSION_NR2(2,1)) && !defined(FOAM_DEV)

       ^



compilation aborted for helpers/printSwakVersion.C (code 2)

make: *** [Make/linux64IccDPOpt/printSwakVersion.o] Error 2

Parser library did not compile OK. No sense continuing as everything else depends on it

I am not sure why I got this problem, and here is my .bashrc file:

Code:

  module load intel-cc/14.0.080

  module load mercurial

  module load python/2.7.5



  module load openmpi/1.6.3

  module load OpenFOAM

I also have tired to follow the instruction from: https://openfoamwiki.net/index.php/I...e_load_is_used

with this, I can compile my own solver, it is OK, but got the error while compiling swak4foam

Thank you very much
Kan

Hi Kan,

Something very wrong is going on with your OpenFOAM installation. swak4Foam's scripts were not able to identify which OpenFOAM version you have installed, which is why you're getting those errors.

After loading all of the necessary modules, please run the following commands and indicate what each one gives you:

Code:

echo $WM_PROJECT_DIR

ls -l  $WM_PROJECT_DIR



which icoFoam



echo $FOAM_APP

ls -l $FOAM_APP



echo $FOAM_SRC

ls -l $FOAM_SRC



echo $WM_PROJECT_VERSION

Best regards,
Bruno

Quote:

Originally Posted by wyldckat (Post 535181)

Code:

echo $WM_PROJECT_DIR

ls -l  $WM_PROJECT_DIR



which icoFoam



echo $FOAM_APP

ls -l $FOAM_APP



echo $FOAM_SRC

ls -l $FOAM_SRC



echo $WM_PROJECT_VERSION

Best regards,
Bruno

Hi Bruno,

Please find the attached results from running your suggested command,

Code:

[kxq564@raijin5 ~]$ echo $WM_PROJECT_DIR

/apps/OpenFOAM/2.2.1

[kxq564@raijin5 ~]$ ls -l  $WM_PROJECT_DIR

total 92

drwxrwxr-x  3 dsr900 apps 20480 May  1  2014 bin

drwxrwxr-x  6 dsr900 apps  4096 Aug 14  2013 etc

drwxrwxr-x 35 dsr900 apps 49152 May  2  2014 include

drwxrwxr-x  4 dsr900 apps 12288 Aug 14  2013 lib

drwxrwxr-x 16 dsr900 apps  4096 Aug 14  2013 tutorials

drwxrwxr-x  6 dsr900 apps  4096 May  2  2014 wmake

[kxq564@raijin5 ~]$ which icoFoam

/apps/OpenFOAM/2.2.1/bin/icoFoam

[kxq564@raijin5 ~]$ echo $FOAM_APP



[kxq564@raijin5 ~]$ ls -l $FOAM_APP

total 28

drwxrwxr-x  3 kxq564 fy8 4096 Sep  1  2014 applications

drwxr-x---  9 kxq564 fy8 4096 Feb 21 14:35 cfcfd3

drwxr-x---  7 kxq564 fy8 4096 Feb 21 14:37 e3bin

drwxr-x---  2 kxq564 fy8 4096 Feb  2 15:05 hidden

drwxr-x---  3 kxq564 fy8 4096 Jan 27 17:43 intel

drwxr-x--- 11 kxq564 fy8 4096 Mar  8 13:15 swak4Foam

drwxrws---  2 kxq564 UQ  4096 Feb  2 15:06 tmp

[kxq564@raijin5 ~]$ echo $FOAM_SRC



[kxq564@raijin5 ~]$ ls -l $FOAM_SRC

total 28

drwxrwxr-x  3 kxq564 fy8 4096 Sep  1  2014 applications

drwxr-x---  9 kxq564 fy8 4096 Feb 21 14:35 cfcfd3

drwxr-x---  7 kxq564 fy8 4096 Feb 21 14:37 e3bin

drwxr-x---  2 kxq564 fy8 4096 Feb  2 15:05 hidden

drwxr-x---  3 kxq564 fy8 4096 Jan 27 17:43 intel

drwxr-x--- 11 kxq564 fy8 4096 Mar  8 13:15 swak4Foam

drwxrws---  2 kxq564 UQ  4096 Feb  2 15:06 tmp

[kxq564@raijin5 ~]$ echo $WM_PROJECT_VERSION



[kxq564@raijin5 ~]$

Seems like $FOAM_APP, $FOAM_SRC and $WM_PROJECT_VERSION don't points to right path.

UPDATE:

Since this is the version definition problem as indicated from bug report, so I directly set the version in my .bashrc file:

Code:

export WM_PROJECT_VERSION=2.2.1

I don't how to define $FOAM_APP plus $FOAM_SRC, so I just ignore them.

Then I recompiled swak4foam, it's now working. But not sure if it's necessary to define $FOAM_APP plus $FOAM_SRC

Cheers,
Kan

Dear Bruno
Thanks for your inputs.
I think that time stamp issues are just warning and do not create any actual error.
I did "touch" and the warnings are gone but still I get same error in compilation.

I do not use any module but just include the the path
source /opt/openfoam231/etc/bashrc
in my bashrc file.

The error was because of not finding the path to mpi libraries as indicated by warning
/usr/bin/ld: warning: libmpi.so.1, needed by /usr/local/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so, not found (try using -rpath or -rpath-link)
I fixed it and now I have swak4foam!

swak4foam could not be installed on the cluster

Hi guys,

Due to the fact that swak4foam could not be installed on the cluster (most of the libraries were compiled but funkySetFields cannot be found and also the groovyBC did not work well), as shown in the following:

Code:

/cineca/prod/opt/applications/openfoam+/v1912/intelmpi--2018--binary/OpenFOAM-v1912+/wmake/rules/linux64Gcc/c++:5: /cineca/prod/opt/applications/openfoam+/v1912/intelmpi--2018--binary/OpenFOAM-v1912+/wmake/rules/linux64Gcc/c++OptBDW: No such file or directory

make: *** No rule to make target `/cineca/prod/opt/applications/openfoam+/v1912/intelmpi--2018--binary/OpenFOAM-v1912+/wmake/rules/linux64Gcc/c++OptBDW'.  Stop.

/cineca/prod/opt/applications/openfoam+/v1912/intelmpi--2018--binary/OpenFOAM-v1912+/wmake/rules/linux64Gcc/c++:5: /cineca/prod/opt/applications/openfoam+/v1912/intelmpi--2018--binary/OpenFOAM-v1912+/wmake/rules/linux64Gcc/c++OptBDW: No such file or directory

/cineca/prod/opt/applications/openfoam+/v1912/intelmpi--2018--binary/OpenFOAM-v1912+/wmake/rules/linux64Gcc/c++:5: /cineca/prod/opt/applications/openfoam+/v1912/intelmpi--2018--binary/OpenFOAM-v1912+/wmake/rules/linux64Gcc/c++OptBDW: No such file or directory

/cineca/prod/opt/applications/openfoam+/v1912/intelmpi--2018--binary/OpenFOAM-v1912+/wmake/rules/linux64Gcc/c++:5: /cineca/prod/opt/applications/openfoam+/v1912/intelmpi--2018--binary/OpenFOAM-v1912+/wmake/rules/linux64Gcc/c++OptBDW: No such file or directory

make: *** No rule to make target `/cineca/prod/opt/applications/openfoam+/v1912/intelmpi--2018--binary/OpenFOAM-v1912+/wmake/rules/linux64Gcc/c++OptBDW'.  Stop.

wmake error: file 'Make/linux64IccDPInt32OptBDW/sourceFiles' could not be created in /galileo/home/userexternal/qyang001/OpenFOAM/qyang001-v1912/swak4Foam/Utilities/makeAxialMesh

In the user's lib, it includes already following src:

Code:

libEulerianInterfacialSedModels.so

libEulerianPpSedModels.so

libgranularRheologySedModel.so

libgroovyBC.so

libgroovyStandardBCs.so

libkineticTheorySedModel.so

libmyturbulenceModels.so

libsimpleCloudFunctionObjects.so

libsimpleFunctionObjects.so

libsimpleLagrangianFunctionObjects.so

libsimpleRegionSolvers.so

libsimpleSearchableSurfaces.so

libsimpleSwakFunctionObjects.so

libswak4FoamParsers.so

libswakChemistryModelFunctionPlugin.so

libswakCloudFunctionObjects.so

libswakCoalCloudAdaptor.so

libswakDynamicMeshFunctionPlugin.so

libswakDynamicMesh.so

libswakFacSchemesFunctionPlugin.so

libswakFiniteArea.so

libswakFunctionObjects.so

libswakFvcSchemesFunctionPlugin.so

libswakFvOptions.so

libswakGeneralLanguageIntegration.so

libswakLagrangianCloudSourcesFunctionPlugin.so

libswakLagrangianParser.so

libswakLocalCalculationsFunctionPlugin.so

libswakLuaIntegration.so

libswakMeshQualityFunctionPlugin.so

libswakMeshWaveFunctionPlugin.so

libswakMRFFunctionPlugin.so

libswakPython3Integration.so

libswakPythonIntegration.so

libswakQuantileFunctionPlugin.so

libswakRadiationModelFunctionPlugin.so

libswakRandomFunctionPlugin.so

libswakScriptableLagrangian.so

libswakShiftFieldFunctionPlugin.so

libswakSourceFields.so

libswakStateMachine.so

libswakSurfacesAndSetsFunctionPlugin.so

libswakThermoTurbFunctionPlugin.so

libswakTopoSources.so

libswakTransportTurbFunctionPlugin.so

libswakVelocityFunctionPlugin.so

libtwoPhaseModel.so

libtwoPhaseTurbulenceModels.so