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[foam-extend.org] Foam Extend 3.2 in ubuntu 16.04 LTS

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Old   May 12, 2016, 13:58
Default Foam Extend 3.2 in ubuntu 16.04 LTS
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Jedrzej Mosiezny
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Good morning. I am experiencing a similar issue in my case.

I was following the instroctions from the website: https://openfoamwiki.net/index.php/I...oam-extend-3.2. and all I get after a couple of hours build is "command not found error" while trying to execute for example icoFoam.

I am usnig Ubuntu 16.04 x64 and to be quite honest I installed it for the sake purpose of using OpenFoam (ver 3.0.1 works perfectly fine) and FoamExtend and feel quite helpless while reading thru logfile

Because the tarball exceeds the filesize limit I hosted the file on my OneDrive and shortened the link with google URL shortener:
https://goo.gl/3ZU8vG

The log itself has around 15MB and the tarball is around 900kB

Thank You
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Old   June 13, 2016, 03:46
Default Foam Extend 3.2 in ubuntu 16.04 LTS
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I want to install foam extend 3.2 on Ubuntu 16.04 LTS
the methods for 14.04 or 15.10 are not succeeding.


Also, Is there any way i can use Paraview 5.0.0 using paraFoam command in fe32?

Thank You very much!!
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Old   June 14, 2016, 03:27
Default No guide for Foam Xtend installation in Ubuntu 16.04
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I want to install foam extend 3.2 on Ubuntu 16.04 LTS
the methods for 14.04 or 15.10 given in wiki link are not a success.

foamInstallationTest
Code:
foamInstallationTest:


Checking basic setup...
-------------------------------------------------------------------------------
Shell:              bash
Host:               iitmech4
OS:                 Linux version 4.4.0-24-generic
-------------------------------------------------------------------------------


Checking main foam-extend env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid      Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /home/iitmech4/foam                      yes       yes
$WM_PROJECT_USER_DIR /home/iitmech4/foam/iitmech4-3.2         no        no
$WM_THIRD_PARTY_DIR  ...ech4/foam/foam-extend-3.2/ThirdParty  yes       yes
-------------------------------------------------------------------------------


Checking the foam-extend env variables set on the PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid Path Crit
-------------------------------------------------------------------------------
$WM_PROJECT_DIR      /home/iitmech4/foam/foam-extend-3.2      yes  yes  yes

$FOAM_APPBIN         ...3.2/applications/bin/linux64GccDPOpt  no        yes
$FOAM_SITE_APPBIN    ...h4/foam/site/3.2/bin/linux64GccDPOpt  no        no
$FOAM_USER_APPBIN    ...3.2/applications/bin/linux64GccDPOpt  no        no
$WM_DIR              .../iitmech4/foam/foam-extend-3.2/wmake  yes  yes  yes
-------------------------------------------------------------------------------


Checking the foam-extend env variables set on the LD_LIBRARY_PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid Path Crit
-------------------------------------------------------------------------------
$FOAM_LIBBIN         .../foam-extend-3.2/lib/linux64GccDPOpt  no        yes
$FOAM_SITE_LIBBIN    ...h4/foam/site/3.2/lib/linux64GccDPOpt  no        no
$FOAM_USER_LIBBIN    ...oam/iitmech4-3.2/lib/linux64GccDPOpt  no        no
$MPI_ARCH_PATH       --------- env variable not set ---------            yes
-------------------------------------------------------------------------------


Third party software
-------------------------------------------------------------------------------
Software Version   Location 
-------------------------------------------------------------------------------
WARNING: gcc version does not match gcc supplied with this release of foam-extend
         Supplied version: 4.3.3
         User version    : 5.3.1
         Minimum required: 4.3.1

gcc      5.3.1    
WARNING:  Conflicting installations:
          foam-extend settings        : /bin/gcc
          current path             : /usr/bin/gcc
          CRITICAL ERROR

gzip     1.6       /bin/gzip                                                
tar      1.28      /bin/tar                                                 
icoFoam           
WARNING:  Conflicting installations:
          foam-extend settings        : /home/iitmech4/foam/foam-extend-3.2/applications/bin/linux64GccDPOpt/icoFoam
          current path             : 
          CRITICAL ERROR

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


Summary
-------------------------------------------------------------------------------
Base configuration ok.

The foam installation contains 2 critical error(s).

Review the output for warning messages and consult 
the installation guide for trouble shooting.

done.
I can't run blockMesh and other commands.

Also, Is there any way i can use Paraview 5.0.0 using paraFoam command in fe32?

Thank You very much!!

Last edited by wyldckat; June 18, 2016 at 17:46. Reason: Changed [QUOTE][/QUOTE] to [CODE][/CODE]
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Old   June 17, 2016, 09:09
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Quote:
Originally Posted by JMosiezny View Post
Good morning. I am experiencing a similar issue in my case.

I was following the instroctions from the website: https://openfoamwiki.net/index.php/I...oam-extend-3.2. and all I get after a couple of hours build is "command not found error" while trying to execute for example icoFoam.

I am usnig Ubuntu 16.04 x64 and to be quite honest I installed it for the sake purpose of using OpenFoam (ver 3.0.1 works perfectly fine) and FoamExtend and feel quite helpless while reading thru logfile

Because the tarball exceeds the filesize limit I hosted the file on my OneDrive and shortened the link with google URL shortener:
https://goo.gl/3ZU8vG

The log itself has around 15MB and the tarball is around 900kB

Thank You
Did you get to install fe32 in 16.04??
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Old   June 17, 2016, 13:20
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Nope. I postponed the task of building FE3.2 after posting here.

Luckilly I doscovered that on OF version 3.0.1 has embedded MRF Properties in rhoPimpleFoam solver and for now I don't need FE3.2

I think I will reach for someones support for this topic in person while OFW11.

Best Regards
JJ
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Old   June 18, 2016, 11:02
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Quote:
Originally Posted by JMosiezny View Post
Nope. I postponed the task of building FE3.2 after posting here.

Luckilly I doscovered that on OF version 3.0.1 has embedded MRF Properties in rhoPimpleFoam solver and for now I don't need FE3.2

I think I will reach for someones support for this topic in person while OFW11.

Best Regards
JJ
Fortunate for you!!

Well i have solved the issue.
I built FE3.2 in 14.04 in other machine and copied all the data in my machine(16.04) and did proper aliasing and Environment Setting.

Fortunately, this is working fine for me. FE32 is working now in 16.04.

though, can't manage to call Paraview 5.0 using paraFoam command.

Last edited by wyldckat; June 18, 2016 at 17:47. Reason: merged posts that were related
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Old   June 18, 2016, 17:48
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Quick answer: I've tested and added the instructions here: https://openfoamwiki.net/index.php/I...u#Ubuntu_16.04

The missing critical detail is that the following command has to be executed before running Allwmake this:
Code:
find src applications -name "*.L" -type f | xargs sed -i -e 's=\(YY\_FLEX\_SUBMINOR\_VERSION\)=YY_FLEX_MINOR_VERSION < 6 \&\& \1='
edit: As for ParaView 5.0, it's easier to install the binary package and follow the idea that is given here: http://www.cfd-online.com/Forums/blo...-openfoam.html
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Last edited by wyldckat; June 18, 2016 at 17:49. Reason: see "edit:"
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Old   June 20, 2016, 13:04
Default thanks that fixed flex
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Follewed appended wiki page on 16.04. I have the following problem.

Apoligies I may be doing something stupid, usually am:

Code:
~/foam/foam-extend-3.2/tutorials/incompressible/icoFoam$ ./Allrun 
Running blockMesh on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavity
Running icoFoam on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavity
Cloning cavityFine case from cavity
Running blockMesh on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavityFine
Running mapFields from cavity to cavityFine
Running icoFoam on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavityFine
Running blockMesh on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavityGrade
Running mapFields from cavityFine to cavityGrade
Running icoFoam on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavityGrade
Cloning cavityHighRe case from cavity
Setting cavityHighRe to generate a secondary vortex
Copying cavity/0* directory to cavityHighRe
Running blockMesh on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavityHighRe
Running icoFoam on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavityHighRe
Running blockMesh on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavityClipped
Running mapFields from cavity to cavityClipped
Running icoFoam on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavityClipped
fluentMeshToFoam: converting mesh elbow/elbow.msh
Running icoFoam on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/elbow
Running foamMeshToFluent on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/elbow
Running foamDataToFluent on /home/eric/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/elbow
~/foam/foam-extend-3.2/tutorials/incompressible/icoFoam$ cd cavity
~/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavity$ ls
0  constant  log.blockMesh  log.icoFoam  system
~/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavity$ cat log.blockMesh 
blockMesh: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
~/foam/foam-extend-3.2/tutorials/incompressible/icoFoam/cavity$ cat log.icoFoam 
icoFoam: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
Then I tried:

Code:
sudo ln -s /usr/lib/libmpi.so.12 /usr/lib/libmpi.so.1
... and it works! Google is such a friend
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Old   June 28, 2016, 19:45
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Hello All,

I had no chance to test the procedure for foam-extend-3.2 but...

I got my hands to foam-extend-4.0 and managed to build the software according to the instructions for version 3.2. The compilation is really quick: in my case 5hrs compared to overnight build for fe-3.2.

Best Regards.
JJ
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Old   August 4, 2016, 05:19
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Hello,

I can't find foam-extend-4.0, where to download foam-extend-4.0 ?

regards,

T.D.
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Old   August 7, 2016, 18:33
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Quote:
Originally Posted by T.D. View Post
I can't find foam-extend-4.0, where to download foam-extend-4.0 ?
Quick answer: "nextRelease" branch of foam-extend 3.2. 4.0 it's still on a pre-release state, which was released for the OFW11.

  1. Use one of the git clone commands from here: https://openfoamwiki.net/index.php/I...om_source_code - and rename the final name to "foam-extend-4.0"
  2. Then go into the "foam-extend-4.0" folder and run:
    Code:
    git checkout nextRelease
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Old   August 25, 2016, 12:40
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This 'sed' hack also works on fedora 22.

Thanks Bruno.
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Old   August 25, 2016, 17:26
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Hi Dan,

Any chance you could also provide the list of system packages you used in Fedora 22? Did you use the same ones from some other instruction list or did you already had the packages you needed installed?

Best regards,
Bruno
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Old   August 29, 2016, 09:46
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I resolve the 'libmpi.so.1: cannot open shared object file: No such file or directory' problem by using your method after updating to 16.04, thanks a lot!
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Old   September 1, 2016, 16:41
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Quote:
Originally Posted by wyldckat View Post
Hi Dan,

Any chance you could also provide the list of system packages you used in Fedora 22? Did you use the same ones from some other instruction list or did you already had the packages you needed installed?

Best regards,
Bruno
I didn't have to install any 'extra' packages for fe-3.2 on this box, though I've been using this box for OpenFOAM simulations going back to 2.1.x.

The general steps I took to get fe-3.2 built on this box.

https://openfoamwiki.net/index.php/I...om_source_code
git clone git://git.code.sf.net/p/foam-extend/foam-extend-3.2
edit etc/bashrc, etc/settings
copy etc/prefs.sh-EXAMPLE tp etc/prefs.sh
edit etc/prefs.sh (already have OpenMPI, CMake, Python, HWLOC, Paraview, bison, flex, Qt)
find src applications -name "*.L" -type f | xargs sed -i -e 's=\(YY\_FLEX\_SUBMINOR\_VERSION\)=YY_FLEX_MINOR_V ERSION < 6 \&\& \1='
sed -iold -e "s=\-liberty==" wmake/rules/*/general
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Old   December 9, 2017, 09:20
Default System OpenMPI should work without additional tweaks
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The libmpi.so issue should not appear if you set up the system openmpi properly in bashrc and prefs.sh. It works for me on Debian Stretch with package libopenmpi2. Here's how libmpi.so is linked in the system installation:

/usr/lib/x86_64-linux-gnu/libmpi.so -> /etc/alternatives/libmpi.so
/etc/alternatives/libmpi.so -> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.20.0.2 (this is the actual library, the others are just symbolic links).

Here's my fe4.0 setup (works for fe-3 as well)...

In bashrc:

Code:
# For AllMake.stage2
#export WM_THIRD_PARTY_USE_OPENMPI_188=1
export WM_THIRD_PARTY_USE_OPENMPI_188=0
.
.
.
# WM_MPLIB = SYSTEMOPENMPI | OPENMPI | MPICH | MPICH-GM | HPMPI | GAMMA | MPI | QSMPI | MVAPICH2
#: ${WM_MPLIB:=OPENMPI}; export WM_MPLIB
: ${WM_MPLIB:=SYSTEMOPENMPI}; export WM_MPLIB
Note that whatever you write in bashrc is usually overridden by the prefs.sh options and I haven't tested whether the 188 statement is really necessary, but I'd rather be consistent if only to show clearly in all setup files we're using the system openmpi.

Now in prefs.sh:

Code:
export WM_MPLIB=SYSTEMOPENMPI
export OPENMPI_DIR=/usr
export OPENMPI_BIN_DIR=$OPENMPI_DIR/bin
#
export OPENMPI_LIB_DIR="`$OPENMPI_BIN_DIR/mpicc --showme:libdirs`"
export OPENMPI_INCLUDE_DIR="`$OPENMPI_BIN_DIR/mpicc --showme:incdirs`"
export OPENMPI_COMPILE_FLAGS="`$OPENMPI_BIN_DIR/mpicc --showme:compile`"
export OPENMPI_LINK_FLAGS="`$OPENMPI_BIN_DIR/mpicc --showme:link`"
.
.
.
#
# For AllMake.stage2
#export WM_THIRD_PARTY_USE_OPENMPI_188=1
#export WM_THIRD_PARTY_USE_OPENMPI_188_ConfigureAdditionalArgs='--enable-mpi-cxx --with-verbs'

Last edited by ziad; December 11, 2017 at 11:54.
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