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source /home/tlcoons/.bashrc: No such file or diirectory

    • Closed Issue created by Terry L. Coons @tlcoons

    This issue is for OpenFoam-2.4.0. I am rumming fedora 23 on a pentium 4 with 4gb ram. I uncompressed both tar files into the OpenFOAM directory. I added the source line to .bashrc file. When I type "source $HOME/.bashrc" I get the following error message. bash: source /home/tlcoons/.bashrc: No such file or directory I tried to execute the command aslo from the home directory and got the same results. Thanks for your help. Terry

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        • Prashant Sonakar Reassigned to @Prashant

          Reassigned to @Prashant

        • Prashant Sonakar Added support label

          Added support label

        • Prashant Sonakar
          Prashant Sonakar @Prashant ·
          Developer

          Could you please elaborate

          • both tar files mean...?

          if possible, please share a snapshot with

          • file list in $HOME
          • content of $HOME/.bashrc (showing lines you edited)
          Edited by Prashant Sonakar
        • Matej Forman
          Matej Forman @matej ·
          Reporter

          I will elaborate little further:

          The reasons why you the system cannot find the .bashrc can be many:

          • you are not running bash shell but zsh, tcsh, csh or something else, where you have other *rc files

          • you are running bash shell, but your settings are in $HOME/.profile and you do not have .bashrc file

          • when saving the .bashrc in your $HOME you have made a typo and saved it under some different name or to the different place.

          • to run OpenFOAM you do not need to enter the line to .bashrc, you can run the command source "installation path to your openfoam - most probably /opt/openfoam/OpenFOAM-2.4/etc/bashrc" on the command line to set the openfoam.

        • Matej Forman
          Matej Forman @matej ·
          Reporter

          To be more specific, you need to:

          dnf groupinstall 'Development Tools'

          dnf groupinstall 'C Development Tools and Libraries'

          dnf install git openmpi openmpi-devel qt-devel qtwebkit-devel zlib-devel wget CGAL-devel
          boost-devel gmp-devel mpfr-devel patch readline-devel ncurses-devel python python-devel

          when installed, you have to load the openmpi module by: module mpi/load openmpi-x86_64 || export PATH=$PATH:/usr/lib64/openmpi/bin

          (this line also include in your .bashrc file)

          You can also consult the instructions from community

          here:https://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-3.0.x/Fedora

          but do not hesitate to get back in touch with us.

          Edited by Matej Forman
        • Matej Forman
          Matej Forman @matej ·
          Reporter

          I can see it now. your command line is wrong. it should be:

          module load mpi/openmpi..... and the rest is OK.

          the ERROR message actually says so, sorry I have not noticed. Please try this version and let us know what happened.

        • Matej Forman
          Matej Forman @matej ·
          Reporter

          OK. let's slow down. First let's figure out what version of openmpi you have installed. type on the command line:

          module avail mpi

          the output in my installation gives:

          mpi/openmpi-x86_64

          then let's try the following on the command line:

          module load mpi/openmpi-x86_64

          will work for me. And since I know I have a 64 bit library, my path will lead to /usr/lib64 accordingly. Please send the output of the first command from your box to resolve where is you mpi hiding.

        • Matej Forman
          Matej Forman @matej ·
          Reporter

          OK. can you please comment out the line loading the module in your .bashrc and post here the output of

          module avail mpi

          I somehow cannot see it here. Thanks

        • Matej Forman
          Matej Forman @matej ·
          Reporter

          I problem sense here. This is really strange, it seems that the installation of openmpi was not successful. If you run:

          dnf info openmpi openmpi-devel

          do you have openmpi and openmpi-devel listed in the "Installed packages" section? Please let me know.

          Edited by Matej Forman
        • Matej Forman
          Matej Forman @matej ·
          Reporter

          OK. this is a good news, because the output makes sense. You do not have openmpi installed on your system. And apparently the x86_64 version is not listed but the i686 is. This is perfectly OK. You have to install the

          dnf install openmpi openmpi-devel

          maybe also run again the whole

          dnf install git openmpi openmpi-devel qt-devel qtwebkit-devel zlib-devel wget CGAL-devel  boost-devel gmp-devel mpfr-devel patch readline-devel ncurses-devel python python-devel

          Please have a look at the output to watch for error messages that some package was not installed. if everything runs fine, after running

          module avail

          you should have a line with mpi/openmpi ...

          copy the bit from the answer mpi/openmpi (and here the specification of the architecture i686 probably) and use it for the

          module load mpi/openmpi     <-......(the rest you will see from the previous command)

          If this runs fine, you may put the module load bit into your bashrc file. then you may proceed to compilation. hope we are finally there.

        • Matej Forman
          Matej Forman @matej ·
          Reporter

          Hi Terry, nearly there,. At the top of your file there are some errors but if you read the info there, you are also adviced to ignore those. Bigger problems comes later on. If I search for keyword ERORR, I found the following line:

          Fatal error: can't create Make/linuxGccDPOpt/polyBoundaryMesh.o: Read-only file system

          And the error message clearly tells you what the problem is: your OpenFOAM is in the directory where you have no write to access. I can fabulate, that you unzipped the tar balls with OpenFOAM under the root access to your home directory, and therefore you are missing writing privileges when compiling as a normal user. You should change the owner or the write access and compile again. Hope this helps.

        • Matej Forman
          Matej Forman @matej ·
          Reporter

          This shows you are missing just another package for installation. Namely the "flex". Please run:

          dnf info flex

          to make sure the flex package is listed among the installed packages. If not, you may install it by

          dnf install flex

          Actually, we have made quite a number of steps here together, and I have to remind you that the gitlab is dedicated to the OpenCFD version of OpenFOAM v3+ and should not be overused for the older versions. You may find lot of help online, regarding the compilation, the link here: http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.4.0/Fedora is really useful. Lot of answers to your problems can be found by searching the online forum, where users are helping each other: http://www.cfd-online.com/Forums/openfoam/ .

          The help we are providing here starts to be in order of small support contract. If I may make a personal comment, one of the most useful skills you have to build to be able to use OpenFOAM is to search for error messages and try to understand them. They typically tell you exactly what is the problem. If you are still lost, googling them usually brings solution.

        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          hometerminalOpenFOAMbashrc Attached are the error message, .bashrc file, and home directory contents as jpg images. Thanks for your help.

        • Prashant Sonakar
          Prashant Sonakar @Prashant ·
          Developer

          Dear User,

          The reason is you are providing the "source xxx" statement with "quotes"

          Try the following?

          [tlcoons@localhost ~]$ source .bashrc

          Also, it seems your MPI setting is improper leading to "bash: mpicc: command not found" in the beginning of shell

          • Comment the OpenFOAM source in your .bashrc file
          • In new shell, check if the error "bash: mpicc: command not found" still appears.
            • if no, review your MPI settings (settings.sh and bashrc files in ~/OpenFOAM/OpenFOAM-2.4.0/etc/)
            • if yes, please revert back.

          Best Regards,

          Prashant

          Edited by Prashant Sonakar
        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          I looked at the settings in the (.bashrc) file in ~/OpenFOAM/OpenFOAM-2.4.0/etc. They appeared to be what the installation instructions said to do. There is no settings.sh file in the directory. How do I correct the mpicc: command not found?

        • Prashant Sonakar
          Prashant Sonakar @Prashant ·
          Developer

          settings.sh is inside ~/OpenFOAM/OpenFOAM-2.4.0/etc/config

          which mpi would you like to use? (system/ thirdparty/...)

          could you post the files bashrc and settings.sh as well?

        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          settings.shbashrc I would like to use the most convenent mpi to work with. Attached are the bashrc and setting.sh files. Thanks again for your help.

        • Prashant Sonakar
          Prashant Sonakar @Prashant ·
          Developer

          Your setup points to usage of system openmpi. (Line 84 of bashrc)

          Line 369 of this setting.sh is set to access mpicc which is not found in your system.

          Please resolve the dependency by installing openmpi package.

          Edited by Prashant Sonakar
        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          bash: mpicc: command not found... cmdTrace.c(713):ERROR:104: 'mpi/load' is an unrecognized subcommand cmdModule.c(415):ERROR:104: 'mpi/load' is an unrecognized subcommand [tlcoons@localhost ~]$

          After I run the following; dnf install git openmpi openmpi-devel qt-devel qtwebkit-devel zlib-devel wget CGAL-devel \ boost-devel gmp-devel mpfr-devel patch readline-devel ncurses-devel python python-devel I got the above error messages. Does it matter where in .bashrc the following line is added? module mpi/load openmpi-x86_64 || export PATH=$PATH:/usr/lib64/openmpi/bin I added it at the end of .bashrc.bashrc

        • Prashant Sonakar
          Prashant Sonakar @Prashant ·
          Developer

          Have you tried to load mpi modules before sourcing OpenFOAM (as mentioned at item 7 in link from Matej)

          Edited by Prashant Sonakar
        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          I moved the load mpi modules to before the source bashrc and this the error message I received: cmdTrace.c(713):ERROR:104: 'mpi/load' is an unrecognized subcommand cmdModule.c(415):ERROR:104: 'mpi/load' is an unrecognized subcommand bash: mpicc: command not found... [tlcoons@localhost ~]$ .bashrc

          I am trying to install OpenFOAM-2.4.0 on a pentium 4 (32 bit) Fedora 23.

          Edited by Terry L. Coons
        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'mpi/openmpi-x86_64' bash: mpicc: command not found... [tlcoons@localhost ~]$ .bashrc I changed the command line in .bashrc and received the error message. Thanks for your help.

        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'mpi/openmpi-x86_64' bash: mpicc: command not found... [tlcoons@localhost ~]$ module avail mpi [tlcoons@localhost ~]$ module load mpi/openmpi-x86_64 ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'mpi/openmpi-x86_64' [tlcoons@localhost ~]$ I received a response from the command module avail mpi

        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          bash: mpicc: command not found... [tlcoons@localhost ~]$ module avail mpi [tlcoons@localhost ~]$

          I received no error message or anything.

        • Matej Forman Status changed to closed

          Status changed to closed

        • Matej Forman Status changed to reopened

          Status changed to reopened

        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          bash: mpicc: command not found... [tlcoons@localhost ~]$ dnf info openmpi openmpi-devel RPM Fusion for Fedora 23 - Nonfree 322 kB/s | 129 kB 00:00
          RPM Fusion for Fedora 23 - Free - Test Updates 517 kB/s | 257 kB 00:00
          Fedora 23 - i386 - Updates 354 kB/s | 20 MB 00:57
          RPM Fusion for Fedora 23 - Free 621 kB/s | 408 kB 00:00
          RPM Fusion for Fedora 23 - Nonfree - Test Updat 241 kB/s | 100 kB 00:00
          Fedora 23 - i386 1.6 MB/s | 39 MB 00:24
          Last metadata expiration check: 0:00:46 ago on Wed May 4 14:42:57 2016. Available Packages Name : openmpi Arch : i686 Epoch : 0 Version : 1.8.8 Release : 5.fc23.1 Size : 3.0 M Repo : updates Summary : Open Message Passing Interface URL : http://www.open-mpi.org/ License : BSD, MIT and Romio Description : Open MPI is an open source, freely available implementation of : both the MPI-1 and MPI-2 standards, combining technologies and : resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, : and PACX-MPI) in order to build the best MPI library available. A : completely new MPI-2 compliant implementation, Open MPI offers : advantages for system and software vendors, application : developers, and computer science researchers. For more : information, see http://www.open-mpi.org/ .

          Name : openmpi-devel Arch : i686 Epoch : 0 Version : 1.8.8 Release : 5.fc23.1 Size : 5.2 M Repo : updates Summary : Development files for openmpi URL : http://www.open-mpi.org/ License : BSD, MIT and Romio Description : Contains development headers and libraries for openmpi.

          [tlcoons@localhost ~]$

        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          I installed the openmpi and openmpi-devel I then installed the whole thing and received the prompt to use --allowerasing I reran it and it installed everything module avail worked module load worked If I have any other problems I'll let you know. Thanks again for all your help.

        • Prashant Sonakar Status changed to closed

          Status changed to closed

        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          The terminal screen reported errors. I copied the screen and made a file (make1log.txt which I compressed to make1log.txt.gz) It appears that some of the source compiled and some didn't. make1log.txt.gz

          Edited by Terry L. Coons
        • Terry L. Coons
          Terry L. Coons @tlcoons ·
          Author

          I started a new terminal last night that was not root. I compiled again and created a make.log file. I ran the command icofoam --help I received the bash error bash: icofoam: command not found ......make.log.gz

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