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[foam-extend.org] Installation problem for foam-extend-3.2 on Ubuntu 14.04

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Old   December 18, 2016, 06:25
Default Installation problem for foam-extend-3.2 on Ubuntu 14.04
  #1
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Ahmet
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Hello everyone,

I am trying to install foam-extend-3.2 on Ubuntu 14.04. I used the instructions written on Wiki. But I got this error after I start to compiling with:
Code:
./Allwmake.firstInstall
Code:
============================================================================
== Configuring Open MPI
============================================================================

*** Startup tests
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking how to create a ustar tar archive... 
ATTENTION! pax archive volume change required.
Ready for archive volume: 1
Input archive name or "." to quit pax.
Archive name >
Anyone help?

Thanks,
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Old   December 18, 2016, 19:39
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Bruno Santos
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Quick answer: I did a quick look for:
Code:
ATTENTION! pax archive volume change required.
and it looks like that there is a problem with file permissions.

Start a new terminal and run:
Code:
cd ~/foam
sudo chown -R $USER:$USER foam-extend-3.2
cd foam-extend-3.2
./Allwmake.firstInstall
Hopefully this will have solved the problem.
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Old   December 19, 2016, 06:09
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Thank you Bruno for quick reply. I tried your suggestions but I still have same error.

This time, I noticed two things before (Bold and red) ==Configuring Open MPI== error part.

Code:
+ ./configure --prefix=/home/ahmet/foam/foam-extend-3.2/ThirdParty/packages/openmpi-1.6.5/platforms/linux64GccDPOpt --exec_prefix=/home/ahmet/foam/foam-extend-3.2/ThirdParty/packages/openmpi-1.6.5/platforms/linux64GccDPOpt --enable-mpirun-prefix-by-default --enable-orterun-prefix-by-default --enable-shared --disable-static --disable-mpi-f77 --disable-mpi-f90 --disable-mpi-cxx --without-slurm --enable-mpi-profile --without-sge --enable-mca-no-build=ras-gridengine,pls-gridengine --disable-vt

============================================================================
== Configuring Open MPI
============================================================================
First, I didn't see openmpi-1.6.5 folder under /ThirdParty/packages.

Code:
ls ThirdParty/packages/
cmake-3.2.2  gcc-4.9.2
Second, I think linux64GccDPOpt is not true. So, I ran these:

Code:
echo export WM_COMPILER=Gcc49 >> etc/prefs.sh
echo export WM_THIRD_PARTY_USE_GCC_492=1  >> etc/prefs.sh
echo export compilerInstall=FOAM >> etc/prefs.sh
 
source etc/bashrc

export QT_BIN_DIR=/usr/bin/qmake-qt4
echo "export QT_BIN_DIR=$QT_BIN_DIR" >> etc/prefs.sh
But, I still got the error. I am adding my foamInstallationTest results below.

Code:
Executing /home/ahmet/foam/foam-extend-3.2/bin/foamInstallationTest:

Checking basic setup...
-------------------------------------------------------------------------------
Shell:              bash
Host:               ----
OS:                 Linux version 4.2.0-27-generic
-------------------------------------------------------------------------------


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

$FOAM_APPBIN         ...2/applications/bin/linux64Gcc49DPOpt  no        yes
$FOAM_SITE_APPBIN    .../foam/site/3.2/bin/linux64Gcc49DPOpt  no        no
$FOAM_USER_APPBIN    ...2/applications/bin/linux64Gcc49DPOpt  no        no
$WM_DIR              /home/ahmet/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         ...oam-extend-3.2/lib/linux64Gcc49DPOpt  no        yes
$FOAM_SITE_LIBBIN    .../foam/site/3.2/lib/linux64Gcc49DPOpt  no        no
$FOAM_USER_LIBBIN    ...foam/ahmet-3.2/lib/linux64Gcc49DPOpt  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    : 4.9.2
         Minimum required: 4.3.1

gcc      4.9.2     ...packages/gcc-4.9.2/platforms/linux64Gcc49DPOpt/bin/gcc
gzip     1.6       /bin/gzip                                                
tar      1.27.1    /bin/tar                                                 
icoFoam           
WARNING:  Conflicting installations:
          foam-extend settings        : /home/ahmet/foam/foam-extend-3.2/applications/bin/linux64Gcc49DPOpt/icoFoam
          current path             : 
          CRITICAL ERROR

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


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

The foam installation contains 1 critical error(s).

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

done.
Any help will be appreciated,
Regards,
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Old   December 21, 2016, 06:40
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Ahmet
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I think I solved the problem with using instructions on OpenFOAM-1.6-ext Wiki page for foam-extend-3.2.

Thank you Bruno,

Note: On the other hand, the solution of our problem may be like on 1 and 2 sites. I didn't completely understand.
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Old   July 2, 2018, 10:56
Default Same problem, several years later...
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Sita Drost
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Hi,


I seem to have the same problem with my installation of foam-extend-4.0. Running foamInstallationTest tells me I have conflicting installations:


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 : 7.3.0
Minimum required: 4.3.1

gcc 7.3.0
WARNING: Conflicting installations:
foam-extend settings : /bin/gcc
current path : /usr/bin/gcc
CRITICAL ERROR

gzip 1.6 /bin/gzip
tar 1.29 /bin/tar
icoFoam ...am-extend-4.0/applications/bin/linux64GccDPOpt/icoFoam
-------------------------------------------------------------------------------




Unfortunately the installation instructions that Ahmet used (installation instructions for OpenFOAM-1.6-ext on Ubuntu 13.10) to fix his problem no longer seem to work in this case. How can I tell foam-extend to use the correct path to gcc?


Thanks in advance!
Sita


UPDATE:
echo $WM_COMPILER_DIR gives me an empty line, which I'm guessing is what causes OpenFOAM to look for gcc in /bin/gcc. I've tried adding export WM_COMPILER_DIR=/usr/ to prefs.sh and settings.sh, and re-running ./Allwmake, but nothing changes. What should I do to set WM_COMPILER_DIR to /usr/?

UPDATE2:
Sorry, forgot to mention that I'm trying to install on Ubuntu 18.04

Last edited by sita; July 3, 2018 at 04:13. Reason: Update
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Old   July 4, 2018, 02:51
Default Solved!
  #6
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Sita Drost
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Yaaay, I've solved it! At least for now, and not in a very pretty way I'm afraid: in etc/settings.sh I copy-pasted the lines


compilerBin=$WM_COMPILER_DIR/bin
compilerLib=$WM_COMPILER_DIR/lib$WM_COMPILER_LIB_ARCH:$WM_COMPILER_DIR/lib



to just after the case statement where the compiler paths are set for the ThirdParty case (lines 130-184), so that those directories are added to the path in the if-statement just after that (I did try to extend the case statement with a System-case, but couldn't get that to work. Been away from OpenFOAM for too long I'm afraid).
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