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-   -   [OpenFOAM.org] OpenFoam installation on CentOs 6.5 without root access (https://www.cfd-online.com/Forums/openfoam-installation/167728-openfoam-installation-centos-6-5-without-root-access.html)

arsalan.dryi March 7, 2016 12:29

OpenFoam installation on CentOs 6.5 without root access
 
Dear Foamers,
I want to compile openFoam 2.3.0 on my University cluster without root access, the operating system of the cluster is CentOs 6.5 and the gcc version is 4.4.7, while i think the minimum gcc version is 4.7 for OpenFoam 2.3.0!
Is there a way to upgrade the gcc version and compile OpenFoam from source code without any root access( The administrator told me to compile anything from source code just in my home folder!) ?
The cluster operating system properties are as follows:
Code:

uname -m
x86_64

uname -a
Linux ssc.ut.ac.ir 2.6.32-431.11.2.el6.x86_64 #1 SMP Tue Mar 25 19:59:55 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

gcc --version
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

flex --version
flex 2.5.35

gcc34 --version
-bash: gcc34: command not found

gcc44 --version
-bash: gcc44: command not found

mpirun --version
-bash: mpirun: command not found

Thank you all for your ideas in advance!
Regards,
Arsalan.

wyldckat March 7, 2016 17:19

Quick question: Have you tried following the instructions given here: http://openfoamwiki.net/index.php/In...HEL#CentOS_6.5 :confused:
If not, then since you do not have root access, you can skip the first 3 steps.

And since you're trying to install on a cluster, you can also skip steps 16 to 18.

arsalan.dryi March 8, 2016 14:25

Quote:

Originally Posted by wyldckat (Post 588541)
Quick question: Have you tried following the instructions given here: http://openfoamwiki.net/index.php/In...HEL#CentOS_6.5 :confused:
If not, then since you do not have root access, you can skip the first 3 steps.

And since you're trying to install on a cluster, you can also skip steps 16 to 18.

Hi Bruno,
Actually i didn't try that because i know that the gcc version on this cluster is 4.4.7 while the minimum gcc version that required for OpenFoam 2.3.0 is 4.7, so i thought that this method does not lead to the good results!
However, if you think that this could be useful, I'll do it and post the results here.
I also read the other posts of you about this problem that you have advised to skip from steps that required root access and post the results, so this is my fault that i did not do it.

Thank you very much for your quick answer.
Regards,
Arsalan.

wyldckat March 13, 2016 15:02

Quote:

Originally Posted by arsalan.dryi (Post 588700)
However, if you think that this could be useful, I'll do it and post the results here.

Quick comment: Like I wrote, if you follow my instructions, hopefully it will build as intended.
Regardless of whether it works or it does not work, then please let me know. Because if it doesn't, it is still possible to build it, because you already have the GCC 4.4 stack installed in that machine.

arsalan.dryi March 13, 2016 18:26

Quote:

Originally Posted by wyldckat (Post 589475)
Regardless of whether it works or it does not work, then please let me know. Because if it doesn't, it is still possible to build it, because you already have the GCC 4.4 stack installed in that machine.

Hi Bruno,
Unfortunately because of the new year holidays i don't have access to the system for two weeks, so I'll do it at the first time after the holidays and post the results here, and i hope that you could help me for build it.

Thank you very much for your attention.
Regards,
Arsalan.

arsalan.dryi April 8, 2016 15:36

Quote:

Originally Posted by wyldckat (Post 589475)
Quick comment: Like I wrote, if you follow my instructions, hopefully it will build as intended.
Regardless of whether it works or it does not work, then please let me know. Because if it doesn't, it is still possible to build it, because you already have the GCC 4.4 stack installed in that machine.

Hi Bruno,
I tried to following the instructions given in the wiki to build OpenFOAM and as expected it didn't work and failed at initial steps (i skipped the first 3 steps). Here is the first error in step 7 :
Code:

[adaryaei@ssc OpenFOAM-2.3.0]$ module load openmpi-x86_64 || export PATH=$PATH:/usr/lib64/openmpi/bin
ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for 'openmpi-x86_64'

However, i continued the process to the final step and uploaded the make.log file in my dropbox for more information.
here is the make.log file download link :
https://www.dropbox.com/s/vnui9qvpde...og.tar.gz?dl=0

(i couldn't attach make.log file here because of the forum's limit of 195.3 KB for gz filetype.)

Thank you very much for your attention.

Regards,
Arsalan.

wyldckat April 10, 2016 16:23

Hi Arsalan,

You will have to either check the instructions page for the cluster you're using, or you need to contact the administrators for the cluster to figure out which MPI toolbox they are using.

I was hoping they were using CentOS' own Open-MPI, but they are apparently using something else. And using the custom Open-MPI that OpenFOAM has got will likely not work in the cluster you're using.

Therefore, you need to ask and/or figure out which MPI the cluster is using and how it's activated, so that you can build OpenFOAM in a way that it can use it.

In addition, there is a particular error that implies that the custom GCC version failed to build properly, namely step #10 failed to work properly. Please check the log file "mkgcc.log" located at "ThirdParty-2.3.0", it should tell us why it didn't work.

Best regards,
Bruno

arsalan.dryi April 11, 2016 18:42

Quote:

Originally Posted by wyldckat (Post 594353)
Hi Arsalan,

You will have to either check the instructions page for the cluster you're using, or you need to contact the administrators for the cluster to figure out which MPI toolbox they are using.

I was hoping they were using CentOS' own Open-MPI, but they are apparently using something else. And using the custom Open-MPI that OpenFOAM has got will likely not work in the cluster you're using.

Therefore, you need to ask and/or figure out which MPI the cluster is using and how it's activated, so that you can build OpenFOAM in a way that it can use it.

In addition, there is a particular error that implies that the custom GCC version failed to build properly, namely step #10 failed to work properly. Please check the log file "mkgcc.log" located at "ThirdParty-2.3.0", it should tell us why it didn't work.

Best regards,
Bruno

Hi Bruno,
I asked the administrators for which mpi version they are using and they told me that using the following command, is it helpful to you?
Code:

module avail

------------------------------ /computing/modules ------------------------------
abaqus/6.12-3          fftw/gcc/2.1.5          matlab/2013a
abaqus/6.13-4          fftw/gcc/3.3.4          mpi/openmpi/gcc/1.8
ansys/v150              fftw/intel/2.1.5        mpi/openmpi/intel/1.8
cmake/2.8.12.2          fftw/intel/3.3.4        namd/intel/2.11
compiler/intel/ips-2013 gromacs/intel/4.6.5
comsol/4.4              lammps/intel/1Feb14

And for the error to building custom GCC version at step #10, the makegcc.log file is as follows :

Code:

---------------
Starting build: gmp-5.1.2

./makeGcc: line 141: cd: /home/adaryaei/OpenFOAM/ThirdParty-2.3.0/gmp-5.1.2: No such file or directory
Error building: gmp-5.1.2

Probably this is because that the connection is refused in step #8, as it shown below :

Code:

[adaryaei@ssc ThirdParty-2.3.0]$ wget "https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getGcc"
--2016-04-12 04:06:12--  https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getGcc
Resolving raw.github.com... 185.31.19.133
Connecting to raw.github.com|185.31.19.133|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://raw.githubusercontent.com/wyldckat/scripts4OpenFOAM3rdParty/master/getGcc [following]
--2016-04-12 04:06:14--  https://raw.githubusercontent.com/wyldckat/scripts4OpenFOAM3rdParty/master/getGcc
Resolving raw.githubusercontent.com... 10.10.34.36
Connecting to raw.githubusercontent.com|10.10.34.36|:443... failed: Connection refused.

Thank you very much again for your attention, i really need this installation because of the high CPU time of simulations for my master thesis.

King regards,
Arsalan.

wyldckat April 12, 2016 19:29

Quick answer: OK, now we're getting closer. Using the instructions on the wiki as a reference: http://openfoamwiki.net/index.php/In...HEL#CentOS_6.5 - do the following steps differently from the wiki:
  1. Steps 1 to 4 can be ignored.
  2. I'm guessing that step #5 worked as intended.
  3. Step #6 is still needed.
  4. In step #7, you should replace this command:
    Code:

    module load openmpi-x86_64
    With this command:
    Code:

    module load mpi/openmpi/gcc/1.8
    Note: there are 2 places where you need to do that change.
  5. In step #8, you will have to do the download manually, instead of relying on wget.
  6. You can replace step #9 with this command:
    Code:

    module load cmake/2.8.12.2
  7. You can try step #10.
    • If the download fails with getGcc, then you will have to download using the files from the download links given by that script.
  8. Same applies to step #11, namely getBinutils might fail to download the necessary package.
  9. Same applies for step #12, namely getBoost might fail to download the package.
  10. Steps #14 and #15 should work as intended.
  11. You can skip steps #16 and #17, because I'm guessing that you will not do post-processing with ParaView within the cluster.
Hopefully this will work as intended.

---

edit: Arsalan made another post a bit related to this topic, but it was more in regards to running in the cluster after the installation went well, therefore it was moved to here: http://www.cfd-online.com/Forums/ope...ble-basis.html

elham usefi May 23, 2016 09:43

step 10
 
Quote:

[*]You can try step #10.
  • If the download fails with getGcc, then you will have to download using the files from the download links given by that script.

Hi bruno,
I have exactly the same question!(but I'm tryin to install openfoam-2.4.0 on centos6.5) and I get the same error in step 10
could u plz explain how can I download the files?and which files?
I downloaded gcc-4.8.4 gmp-5.1.2 mpfr-3.1.2 mpc-1.0.1 files from

http://mpfr.loria.fr/mpfr-3.1.2/mpfr-3.1.2.tar.bz2
ftp://208.118.235.20/gnu/gcc/gcc-4.8.4/gcc-4.8.4.tar.gz
https://gmplib.org/download/gmp-5.1.2/gmp-5.1.2.tar.bz2
http://www.multiprecision.org/mpc/do...c-1.0.1.tar.gz

and then extracted them in ThirdParty-2.4.0 and ran step 10 but it didn't work and I got the same error:

No such file or directory
Error building: gmp-5.1.2

thanks in advance :)

elham usefi May 26, 2016 05:09

done!
 
Quote:

Quote:

Originally Posted by elham usefi (Post 601339)
Hi bruno,
I have exactly the same question!(but I'm tryin to install openfoam-2.4.0 on centos6.5) and I get the same error in step 10
could u plz explain how can I download the files?and which files?
I downloaded gcc-4.8.4 gmp-5.1.2 mpfr-3.1.2 mpc-1.0.1 files from

http://mpfr.loria.fr/mpfr-3.1.2/mpfr-3.1.2.tar.bz2
ftp://208.118.235.20/gnu/gcc/gcc-4.8.4/gcc-4.8.4.tar.gz
https://gmplib.org/download/gmp-5.1.2/gmp-5.1.2.tar.bz2
http://www.multiprecision.org/mpc/do...c-1.0.1.tar.gz

and then extracted them in ThirdParty-2.4.0 and ran step 10 but it didn't work and I got the same error:

No such file or directory
Error building: gmp-5.1.2

thanks in advance :)


Hi I found the solution arsalan.dryi sent me the correct links
thanks :)

charitonas May 30, 2016 14:35

Hi guys,

I have installed the OpenFOAM 3.0.0 in a cluster (Centos 6.7) and i can run it on a single processor (6 cores). However, when i try to run it in through the qsub in got an error:

rhoCentralFoam: command not found.

Does anyone knows what should i do?

Thank you in advance

arsalan.dryi May 30, 2016 15:49

Quote:

Originally Posted by charitonas (Post 602502)
Hi guys,

I have installed the OpenFOAM 3.0.0 in a cluster (Centos 6.7) and i can run it on a single processor (6 cores). However, when i try to run it in through the qsub in got an error:

rhoCentralFoam: command not found.

Does anyone knows what should i do?

Thank you in advance

Ok, at first you should load up OpenFOAM's environment at your qsub file, for detailed information read this thread : http://www.cfd-online.com/Forums/ope...ble-basis.html

Regards,
Arsalan.

charitonas May 30, 2016 16:11

Hi Arsalan,

Thank you for your suggestion. I have tried that but it still not recognise the OpenFOAM as loaded and i don't know why.My error is:

gcc: error: unrecognized command line option '--showme:link'
/opt/gridengine/default/spool/compute-0-0/job_scripts/768: line 53: rhoCentralFoam: command not found

Can you think why i got this error?

Thanks again

arsalan.dryi May 30, 2016 16:23

Quote:

Originally Posted by charitonas (Post 602515)
Hi Arsalan,

Thank you for your suggestion. I have tried that but it still not recognise the OpenFOAM as loaded and i don't know why.My error is:

gcc: error: unrecognized command line option '--showme:link'
/opt/gridengine/default/spool/compute-0-0/job_scripts/768: line 53: rhoCentralFoam: command not found

Can you think why i got this error?

Thanks again

Ok, please attach your job script and use the "module avail" command and post the result here for more detailed information.

Regards.

charitonas May 30, 2016 16:33

1 Attachment(s)
When i press module avail i get :

[cc535@rocks OpenFOAM]$ module avail

-------------------------------------------------------------------------------------- /usr/share/Modules/modulefiles ---------------------------------------------------------------------------------------
dot module-git module-info modules null opt-python use.own

--------------------------------------------------------------------------------------------- /etc/modulefiles ----------------------------------------------------------------------------------------------
mpich-x86_64 openmpi-x86_64

Thanks

charitonas May 31, 2016 06:00

Hi,

I managed to find that the problem is with the parallel environment since openmpi is not install. Do you know if i can run in parallel with MPICH?how?

Thanks again

Wang Wei June 5, 2016 01:03

Hi, I'm trying to install openfoam v3.0.1 in my home directory, and I use this instruction page http://openfoamwiki.net/index.php/In...HEL#CentOS_6.7
But I got errors:
Code:

module load openmpi-x86_64 || export PATH=$PATH:/usr/lib64/openmpi/bin
ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for 'openmpi-x86_64'
 source $HOME/OpenFOAM/OpenFOAM-3.0.1/etc/bashrc WM_LABEL_SIZE=64 foamCompiler=ThirdParty

Warning in /home/nus/e0013038/OpenFOAM/OpenFOAM-3.0.1/etc/config/settings.sh:
    Cannot find /home/nus/e0013038/OpenFOAM/ThirdParty-3.0.1/platforms/linux64/gcc-4.8.4 installation.
    Please install this compiler version or if you wish to  use the system compiler,
    change the 'foamCompiler' setting to 'system'

-bash: mpicc: command not found

It seems there is something wrong with "mpicc". Should I change the commands in step 7?
there is some information maybe helpful
Code:

module avail

------------------------------------------------------- /cm/local/modulefiles -------------------------------------------------------
cluster-tools/7.1        gcc/5.1.0                mvapich2/mlnx/gcc/64/2.1  pbspro/13.0.1.152391      use.own
cmd                      ipmitool/1.8.15          null                      pbspro/13.1.7            version
dot                      module-git                openldap                  pbspro/default
freeipmi/1.4.8            module-info              openmpi/mlnx/gcc/64/1.8.6 shared

------------------------------------------------------ /cm/shared/modulefiles -------------------------------------------------------
allinea/forge/6.0                    gcc/4.9.3                            mpiblast/1.6.0
ambertools/15update6                  gdb/7.9                              ncbi-blast/2.3.0+
ansys                                gmp/6.1.0                            nci-blast/2.3.0+
aspera/3.5.4.102989                  gnuplot/5.0.3                        netcdf/4.4.0/xe_2016/parallel
autoconf/2.69                        guile/2.0.11                          netcdf-fortran/4.4.3/xe_2016/parallel
autogen/5.18.7                        hdf5/1.8.16/xe_2016/parallel          nwchem/6.6
automake/1.15                        hdf5/1.8.16/xe_2016/serial            openfoam/3.0.1/xe_2016/parallel
bcl2fastq/2.17.1.14                  hmmer/3.0                            openmpi/intel/1.10.2
bedtools/2.25                        http_proxy                            parallel/20160222
binutils/2.26                        impi/5.0.3                            pbs-drmaa/1.0.19
bio/all                              impi/5.1.2                            pbspro/13.1.7
boost/1.60.0/xe_2016/parallel        intel-cluster-checker/2.2.2          pbspro/default
bowtie/1.1.2                          intel-cluster-runtime/ia32/3.7        perl5lib
bowtie2/2.29                          intel-cluster-runtime/intel64/3.7    pnetcdf/1.7.0/xe_2016/parallel
bwa/0.7.13                            intel-cluster-runtime/mic/3.7        python/2.7.11
cmake/3.5.0-rc3                      intel-tbb-oss/ia32/43_20150424oss    quantum-espresso/5.3.0
cmgui/7.1                            intel-tbb-oss/intel64/43_20150424oss  quantum-espresso/5.4.0/gpu
compiler/intel/16.0.1                isl/0.14                              quantum-espresso/5.4.0/mpi+openmp
composerxe/2015.3.187                lammps/16Feb16                        quantum-espresso/5.4.0/parallel
composerxe/2016.1.150                libgd/2.1.1                          R/3.2.4
cuda/6.5                              libtool/2.4.6                        samtools/1.3
cuda/7.0                              libunistring/0.9.5                    scotch/6.0.3/xe_2016/parallel
cuda/7.5                              lzip/1.18-rc2                        szip/2.1
cufflinks/2.2.1                      mkl/gcc                              tophat/2.1.1
default-environment                  mpc/1.0.3                            xz/5.2.2
dejagnu/1.5.3                        mpfr/3.1.4
fftw/3.3.4/xe_2016/parallel          mpi/intel


charitonas June 5, 2016 07:05

Hi,

First of all from what i can see you are trying to load the openmpi-x86_64 but it doesn't exist. Please try to contact the administrator (if its not you) and install the openmpi-x86_64. After that, when you press module avail you will see that the openmpi-x86_64 is on the available modules.In addition i think that there is not any mpicc installed. Try first installing the openmpi-x86_64 and then we can see the other errors.

Chariton

Wang Wei June 6, 2016 23:54

Quote:

Originally Posted by charitonas (Post 603427)
Hi,

First of all from what i can see you are trying to load the openmpi-x86_64 but it doesn't exist. Please try to contact the administrator (if its not you) and install the openmpi-x86_64. After that, when you press module avail you will see that the openmpi-x86_64 is on the available modules.In addition i think that there is not any mpicc installed. Try first installing the openmpi-x86_64 and then we can see the other errors.

Chariton

Thank you for your reply, Chariton! I sent an email to the administrator, but no reply yet. I'll post results after I solve the 'openmpi-x86_64' problem.


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