[JBrake]

I have read dozens of threads on this, but cannot find a fix to get any of the three tutorials to run in fsiFoam on foam-extend-4.0.

For example, after following the intructions here (https://openfoamwiki.net/index.php/E...oam-extend_3.0) to run the tutorial HronTurekFsi3, I get the following output:

Running blockMesh on /home/jbrakefi/foam/jbrakefi-4.0/FluidSolidInteraction/run/fsiFoam/HronTurekFsi3/fluid
Running setSet on /home/jbrakefi/foam/jbrakefi-4.0/FluidSolidInteraction/run/fsiFoam/HronTurekFsi3/fluid
Running setsToZones on /home/jbrakefi/foam/jbrakefi-4.0/FluidSolidInteraction/run/fsiFoam/HronTurekFsi3/fluid
Running blockMesh on /home/jbrakefi/foam/jbrakefi-4.0/FluidSolidInteraction/run/fsiFoam/HronTurekFsi3/fluid
Running setSet on /home/jbrakefi/foam/jbrakefi-4.0/FluidSolidInteraction/run/fsiFoam/HronTurekFsi3/fluid
Running setsToZones on /home/jbrakefi/foam/jbrakefi-4.0/FluidSolidInteraction/run/fsiFoam/HronTurekFsi3/fluid
/bin/sh: 1: /home/jbrakefi/foam/foam-extend-4.0/wmake/bin/linux64Gcc/wmkdep: not found
SOURCE=hronTurekReport.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wno-deprecated -Wall -Wextra -Wno-unused-parameter -Wnon-virtual-dtor -Wunused-local-typedefs -Werror -Wredundant-decls -Wcast-align -Wmissing-declarations  -Wswitch-enum -Winvalid-pch -Wredundant-decls -Wformat=2 -Wmissing-format-attribute -Wformat-nonliteral -O3  -DNoRepository -ftemplate-depth-200 -std=c++11     -I/home/jbrakefi/foam/jbrakefi-4.0/FluidSolidInteraction/src/fluidSolidInteraction/lnInclude     -I/home/jbrakefi/foam/jbrakefi-4.0/FluidSolidInteraction/src/ThirdParty/eigen3     -I/home/jbrakefi/foam/foam-extend-4.0/src/finiteVolume/lnInclude     -I/home/jbrakefi/foam/foam-extend-4.0/src/finiteArea/lnInclude     -I/home/jbrakefi/foam/foam-extend-4.0/src/meshTools/lnInclude     -I/home/jbrakefi/foam/foam-extend-4.0/src/dynamicMesh/dynamicFvMesh/lnInclude     -I/home/jbrakefi/foam/foam-extend-4.0/src/lagrangian/basic/lnInclude -IlnInclude -I. -I/home/jbrakefi/foam/foam-extend-4.0/src/foam/lnInclude -I/home/jbrakefi/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/hronTurekReport.o
In file included from hronTurekReport.C:29:0:
hronTurekReport.H:41:28: fatal error: functionObject.H: No such file or directory
compilation terminated.
hronTurekReport.dep:3: recipe for target 'Make/linux64GccDPOpt/hronTurekReport.o' failed
make: *** [Make/linux64GccDPOpt/hronTurekReport.o] Error 1
Running fsiFoam on /home/jbrakefi/foam/jbrakefi-4.0/FluidSolidInteraction/run/fsiFoam/HronTurekFsi3/fluid

I get similar errors when trying to run beamInCrossFlow.

The 3dTube doesn't give me an error but seems to do nothing. When I open the log.fsiFoam, it reads "./Allrun: 55: ./Allrun: fsiFoam: not found"

[JBrake]

I may not have installed/compiled foam-extend-4.0 correctly. I followed the instructions here: https://openfoamwiki.net/index.php/I...u#Ubuntu_16.04

These instructions seem incomplete when compared to that of installing on Linux: https://openfoamwiki.net/index.php/I...oam-extend-4.0

What instructions do I need to follow? I tried running a tutorial on fe4.0 and it was missing an ./Allrun and I couldn't even get blockMesh to work.

[Daniel_Khazaei]

Originally Posted by JBrake

I may not have installed/compiled foam-extend-4.0 correctly. I followed the instructions here: https://openfoamwiki.net/index.php/I...u#Ubuntu_16.04

These instructions seem incomplete when compared to that of installing on Linux: https://openfoamwiki.net/index.php/I...oam-extend-4.0

What instructions do I need to follow? I tried running a tutorial on fe4.0 and it was missing an ./Allrun and I couldn't even get blockMesh to work.

Hi,

Those links you have posted are complementary.
The first link contains prerequisites that are needed before heading to the second link which actually contain the instruction to compile foam-extend-4.0.

I think you have not compiled the source code yet, refer to section 1.2 which describe everything step by step.

[JBrake]

Thank you for the reply. I got up until the ./Allwmake.firstInstall, and it seems stuck on the following with no indication as to how long it will take. If more than an hour goes by, should I kill it and start over or try to find what went wrong?

make: Nothing to be done for 'all'.

This system rpm command: rpm --force-debian

========================================
Starting ThirdParty Allwmake.pre
========================================


This system rpm command: rpm --force-debian

========================================
Starting ThirdParty AllMake: Stage1
========================================

Building bison 2.7
Package name      : bison-2.7
Package URL       : http://ftpmirror.gnu.org/bison/bison-2.7.tar.gz
RPM spec file name: bison-2.7.spec
RPM file name     :
Additional flags  :
Updating the ThirdParty environment variables before building package bison-2.7
RPM file name     : /home/jbrakefi/foam/foam-extend-4.0/ThirdParty/rpmBuild/RPMS/x86_64/bison-2.7-linux64GccDPOpt.x86_64.rpm
Making package bison-2.7 using RPM.
Building package bison-2.7 using SPEC file : bison-2.7.spec. Optional args:

[Daniel_Khazaei]

Originally Posted by JBrake

Thank you for the reply. I got up until the ./Allwmake.firstInstall, and it seems stuck on the following with no indication as to how long it will take. If more than an hour goes by, should I kill it and start over or try to find what went wrong?

It depends on your config and PC resources.
Could you post the complete build log?

It takes less than an hour on my PC to build Third-party utilities + foam-extend source code with eight 4.0GHz cores.

[JBrake]

Originally Posted by Daniel_Khazaei

It depends on your config and PC resources.
Could you post the complete build log?

What is a complete build log and how to I find it? I left it going overnight but seems to have made no progress and is still stuck on "Building package bison-2.7 using SPEC file : bison-2.7.spec. Optional args:"

[JBrake]

For now, I am attempting to run ./Allwmake since maybe the "first time" can't be run again after it fails. Should I have tried ./Allclean first?

It has been running for a while now (~30 minutes) but at least it is doing things and printing to the terminal.

I am also looking into installing the Windows version. I am using Windows 10, and since previously I was using OpenFoam standard I could not run it directly on Windows and instead have been using the Bash on Ubuntu on Windows.

[JBrake]

It looks like installing on Windows won't be any easier, and the instructions for that (https://openfoamwiki.net/index.php/I...oam-extend-4.0) mention that it isn't "fully tested or validated". Is it worth my time trying this route?

Looking through the tutorial cases in foam-extend-4.0, why are no ./Allrun files included? There's one ./Allrun in the root of tutorials. How are you supposed to run these?

I still think I did not compile correctly, because if I try "blockMesh" inside any of the tutorials, it says command not found.

[JBrake]

Is there a way to start over and remove foam-extend and fsiFoam, neither of which are working? I don't know if simply deleting all the files will work, but using ./Allclean gives this output:

./Allclean: line 2: rmdepall: command not found
./Allclean: line 3: wcleanLnIncludeAll: command not found

I really don't have the computer skills required to do manual installations of open source tools like this. If the instructions don't work, I'm at a loss.

[aow]

Based on the fact that wcleanLnIncludeAll isn't working, I'm wondering if you maybe forgot to source the foam-extend-4.0 bashrc file before executing the ./Allclean command?

[JBrake]

I got the ./Allclean command to work now, but still cannot get ./Allwmake.firstInstall to get beyond "Building package bison-2.7 using SPEC file : bison-2.7.spec. Optional args:".

How do I truly get rid of everything and start fresh?

[aow]

Since you're compiling foam-extend using source files I believe you can just delete the directories where you installed it based on this post.

[JBrake]

I deleted everything and tried from the beginning. After I got to "./Allwmake.firstInstall" things seemed at first to go better, as I got more output, but it also stopped after a while with no indication as to how long it will be stuck:

gcc -m64  -Wall -O3   -fPIC dirToString.c -o /home/jbrakefi/foam/foam-extend-4.0/wmake/bin/linux64Gcc/dirToString
flex wmkdep.l
gcc -m64  -Wall -O3   -fPIC lex.yy.c -o /home/jbrakefi/foam/foam-extend-4.0/wmake/bin/linux64Gcc/wmkdep
lex.yy.c:1406:17: warning: ‘yyunput’ defined but not used [-Wunused-function]
     static void yyunput (int c, char * yy_bp )
                 ^
lex.yy.c:1449:16: warning: ‘input’ defined but not used [-Wunused-function]
     static int input  (void)
                ^

This system rpm command: rpm --force-debian

========================================
Starting ThirdParty Allwmake.pre
========================================


This system rpm command: rpm --force-debian

========================================
Starting ThirdParty AllMake: Stage1
========================================

Building bison 2.7
Package name      : bison-2.7
Package URL       : http://ftpmirror.gnu.org/bison/bison-2.7.tar.gz
RPM spec file name: bison-2.7.spec
RPM file name     :
Additional flags  :
Updating the ThirdParty environment variables before building package bison-2.7
RPM file name     : /home/jbrakefi/foam/foam-extend-4.0/ThirdParty/rpmBuild/RPMS/x86_64/bison-2.7-linux64GccDPOpt.x86_64.rpm
Download bison-2.7.tar.gz from : http://ftpmirror.gnu.org/bison/bison-2.7.tar.gz
--2019-04-18 11:42:49--  http://ftpmirror.gnu.org/bison/bison-2.7.tar.gz
Resolving ftpmirror.gnu.org (ftpmirror.gnu.org)... 209.51.188.200, 2001:470:142:5::200
Connecting to ftpmirror.gnu.org (ftpmirror.gnu.org)|209.51.188.200|:80... connected.
HTTP request sent, awaiting response... 302 Moved Temporarily
Location: http://ftp.wayne.edu/gnu/bison/bison-2.7.tar.gz [following]
--2019-04-18 11:42:50--  http://ftp.wayne.edu/gnu/bison/bison-2.7.tar.gz
Resolving ftp.wayne.edu (ftp.wayne.edu)... 141.217.0.199
Connecting to ftp.wayne.edu (ftp.wayne.edu)|141.217.0.199|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3137885 (3.0M) [application/x-gzip]
Saving to: ‘bison-2.7.tar.gz’

bison-2.7.tar.gz              100%[=================================================>]   2.99M   805KB/s    in 3.8s

2019-04-18 11:42:54 (805 KB/s) - ‘bison-2.7.tar.gz’ saved [3137885/3137885]

Making package bison-2.7 using RPM.
Building package bison-2.7 using SPEC file : bison-2.7.spec. Optional args:
tools/makeThirdPartyFunctionsForRPM: line 163: 30204 Segmentation fault      (core dumped) rpmbuild --define "_topdir $buildBase" --dbpath $buildBase/rpmDB -bb ./SPECS/$specFile "$@"
Installing package: bison-2.7
  Uninstalling bison-2.7 using RPM: bison-2.7-linux64GccDPOpt.x86_64
  Installing bison-2.7 using RPM file: /home/jbrakefi/foam/foam-extend-4.0/ThirdParty/rpmBuild/RPMS/x86_64/bison-2.7-linux64GccDPOpt.x86_64.rpm
error: open of /home/jbrakefi/foam/foam-extend-4.0/ThirdParty/rpmBuild/RPMS/x86_64/bison-2.7-linux64GccDPOpt.x86_64.rpm failed: No such file or directory
Done installing package

========================================
Done ThirdParty AllMake: Stage1
========================================


This system rpm command: rpm --force-debian

========================================
Starting ThirdParty AllMake: Stage2
========================================

Building openmpi 1.8.8
Package name      : openmpi-1.8.8
Package URL       : http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz
RPM spec file name: openmpi-1.8.8.spec
RPM file name     :
Additional flags  : --define
Updating the ThirdParty environment variables before building package openmpi-1.8.8
RPM file name     : /home/jbrakefi/foam/foam-extend-4.0/ThirdParty/rpmBuild/RPMS/x86_64/openmpi-1.8.8-linux64GccDPOpt.x86_64.rpm
Download openmpi-1.8.8.tar.gz from : http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz
--2019-04-18 11:42:54--  http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz
Resolving www.open-mpi.org (www.open-mpi.org)... 192.185.39.252
Connecting to www.open-mpi.org (www.open-mpi.org)|192.185.39.252|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz [following]
--2019-04-18 11:42:54--  https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz
Connecting to www.open-mpi.org (www.open-mpi.org)|192.185.39.252|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://download.open-mpi.org/release/open-mpi/v1.8/openmpi-1.8.8.tar.gz [following]
--2019-04-18 11:42:55--  https://download.open-mpi.org/release/open-mpi/v1.8/openmpi-1.8.8.tar.gz
Resolving download.open-mpi.org (download.open-mpi.org)... 99.84.239.72, 99.84.239.96, 99.84.239.75, ...
Connecting to download.open-mpi.org (download.open-mpi.org)|99.84.239.72|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19718799 (19M) [application/x-tar]
Saving to: ‘openmpi-1.8.8.tar.gz’

openmpi-1.8.8.tar.gz          100%[=================================================>]  18.80M  48.4MB/s    in 0.4s

2019-04-18 11:42:55 (48.4 MB/s) - ‘openmpi-1.8.8.tar.gz’ saved [19718799/19718799]

Making package openmpi-1.8.8 using RPM.
Building package openmpi-1.8.8 using SPEC file : openmpi-1.8.8.spec. Optional args: --define _configureAdditionalArgs "$WM_THIRD_PARTY_USE_OPENMPI_188_ConfigureAdditionalArgs"

[aow]

How long has your system been trying to compile OpenMPI? Based on FAQ Item 37 in this openmpi.org FAQ list, it seems like compiling OpenMPI may take a long time for compiling things using the F90 fortran standard.

[JBrake]

One hour later, still going.

[JBrake]

I have had the same kinds of issues as on this thread, and so I'm hoping someone can help me finally get foam-extend-4.0 running on my bash on ubuntu on windows subsystem.

Sometimes it gets stuck on Stage 1 while building package bison-2.7, but if I delete everything and start over, it gets stuck on Stage 2 building package openmpi-1.8.8:

========================================
Starting ThirdParty AllMake: Stage2
========================================

Building openmpi 1.8.8
Package name      : openmpi-1.8.8
Package URL       : http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz
RPM spec file name: openmpi-1.8.8.spec
RPM file name     :
Additional flags  : --define
Updating the ThirdParty environment variables before building package openmpi-1.8.8
RPM file name     : /home/jbrakefi/foam/foam-extend-4.0/ThirdParty/rpmBuild/RPMS/x86_64/openmpi-1.8.8-linux64GccDPOpt.x86_64.rpm
Download openmpi-1.8.8.tar.gz from : http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz
--2019-04-19 13:44:58--  http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz
Resolving www.open-mpi.org (www.open-mpi.org)... 192.185.39.252
Connecting to www.open-mpi.org (www.open-mpi.org)|192.185.39.252|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz [following]
--2019-04-19 13:44:59--  https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz
Connecting to www.open-mpi.org (www.open-mpi.org)|192.185.39.252|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://download.open-mpi.org/release/open-mpi/v1.8/openmpi-1.8.8.tar.gz [following]
--2019-04-19 13:44:59--  https://download.open-mpi.org/release/open-mpi/v1.8/openmpi-1.8.8.tar.gz
Resolving download.open-mpi.org (download.open-mpi.org)... 13.32.252.196, 13.32.252.3, 13.32.252.178, ...
Connecting to download.open-mpi.org (download.open-mpi.org)|13.32.252.196|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19718799 (19M) [application/x-tar]
Saving to: ‘openmpi-1.8.8.tar.gz’

openmpi-1.8.8.tar.gz          100%[=================================================>]  18.80M  46.2MB/s    in 0.4s

2019-04-19 13:45:00 (46.2 MB/s) - ‘openmpi-1.8.8.tar.gz’ saved [19718799/19718799]

Making package openmpi-1.8.8 using RPM.
Building package openmpi-1.8.8 using SPEC file : openmpi-1.8.8.spec. Optional args: --define _configureAdditionalArgs "$WM_THIRD_PARTY_USE_OPENMPI_188_ConfigureAdditionalArgs"

This is what's in my prefs.sh:

export WM_THIRD_PARTY_USE_BISON_27=1
export QT_BIN_DIR=/path/to/qmake_directory
export QT_BIN_DIR=/usr/bin/

[JBrake]

After installing both bison and openmpi manually, it gets stuck at the very next installation in Stage 3, which is metis.

It always gets stuck after "Building package metis-5.1.0 using SPEC file : metis-5.1.0.spec. Optional args:"

So this is not an issue with an individual package. How do I troubleshoot why it always gets stuck at "Optional args:"??

[russel60]

Hi JBrake,

I will start by saying that I am no expert, and got mine to work mostly through random guessing. Here are some things that I might suggest to try, in no particular order:

1. Try running individual wmake's for each of the stages
2. Assume that everything is already installed and see if you can run a job. I remember being suprised that everything worked when I had previously convinced myself that I needed to do more installation.
3. Restart your computer and try again.

If those suggestions don't do it for you, I'm afraid I am out of options. Maybe we will get graced by Wyldcat and he can help you debug further.

[wyldckat]

Quick request @JBrake: I need to know the exact Ubuntu version you are using. Please run the following command:

cat /etc/lsb-release

Because instructions that work for Ubuntu 16.04 do not work on 18.04 and vice-versa... furthermore, one small mistake is enough to break the whole installation sequence...


edit: Furthermore, if the link in the first post was correct, then the original issue seemed to be because the wrong version of the FSI toolkit (meant for foam-extend 3.0) was being used with foam-extend 4.0...

[JBrake]

I am using Ubuntu 16.04 on Bash on Windows (subsystem).