[swak4Foam] swak4Foam installaton issue on cluster

canopus · March 2, 2015, 07:53

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)?

nwpukaka · March 4, 2015, 02:26

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

canopus · March 4, 2015, 10:05

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

wyldckat · March 7, 2015, 20:27

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

nwpukaka · March 7, 2015, 22:29

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

wyldckat · March 8, 2015, 09:06

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

nwpukaka · March 8, 2015, 19:37

Quote:

Originally Posted by wyldckat

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

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

canopus · March 9, 2015, 10:37

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.

canopus · March 10, 2015, 11:04

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!

qi.yang@polimi.it · May 25, 2021, 13:57

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

March 7, 2015, 20:27		#4
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,982 Blog Entries: 45 Rep Power: 128	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 __________________ OpenFOAM: FAQ \| Getting started Forum: How to get help, to post code/output and forum guide Read this before sending me PM

March 8, 2015, 09:06		#6
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,982 Blog Entries: 45 Rep Power: 128	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 __________________ OpenFOAM: FAQ \| Getting started Forum: How to get help, to post code/output and forum guide Read this before sending me PM

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March 4, 2015, 02:26		#2
nwpukaka Member Kan Join Date: Feb 2014 Location: Australia Posts: 54 Rep Power: 12	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

March 4, 2015, 10:05		#3
canopus Member SM Join Date: Dec 2010 Posts: 97 Rep Power: 15	Unfortunately not so far. Trying to get hold of sys admin and running things on desktop for time being!

March 9, 2015, 10:37		#8
canopus Member SM Join Date: Dec 2010 Posts: 97 Rep Power: 15	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.

March 10, 2015, 11:04		#9
canopus Member SM Join Date: Dec 2010 Posts: 97 Rep Power: 15	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!