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Old   February 7, 2013, 09:26
Default ThirdParty compilation error during OF-1.6-ext installation
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Hi,

I want to install OF 1.6-ext. I am currently trying the installation on ubuntu natty (i686).

I downloaded from unofficial git repository suggested by Bruno. I am following installation instructions from http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-1.6-ext/Ubuntu.
I am facing error while compiling thirdparty in its 3rd stage. To be more specific, the error is in the installation of scotch 5.1.10b. I am attaching the log file here.
I downloaded all the required packages (metis, scotch, parmetis etc.) manually and placed the tar files inside /ThirdParty/rpmBuild/sources. But, as you can see from the log file scotch is getting downloaded again. This did not happen with other packages.

Note : the log file attached here ends abruptly while downloading parmetis as I have stopped the compilation.
I am already using OF 201 but I need this extend desperately now. Btw, I have 201 version installed in another machine.
Instant help would be really appreciated.
thanks,

achyutan
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File Type: gz log.tar.gz (2.7 KB, 2 views)

Last edited by achyutan; February 7, 2013 at 09:47. Reason: want to change the title
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Old   February 7, 2013, 09:58
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Hi achyutan,

Instant help is difficult to give, specially since I don't have a VM with Ubuntu 11.04 with me.

But from the log, it looks like you didn't install "zlib1g-dev":
Code:
sudo apt-get install zlib1g-dev
Best regards,
Bruno
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Old   February 7, 2013, 10:15
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Hi Bruno,

thanks for the quick reply. I am sorry for that statement ; I meant as soon as possible.

Now, I have installed zlib1g-dev and still getting some error in scotch installation. It seems like some 'mpicc command not found'.
I have attached the corresponding log file.







achyutan
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Old   February 7, 2013, 18:34
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Hi achyutan,

Go into 1.6-ext's ThirdParty folder and run:
Code:
./AllMake.stage2
What does it output? Because mpicc should be one of the binaries that are build during this stage!

Where did you get your source code of 1.6-ext?

Best regards,
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Old   February 11, 2013, 06:12
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Hi Bruno,

I downloaded the repository pack from : https://github.com/ogoe/OpenFOAM-1.6-ext
I did not get any error during stage2 compilation. But, it installed only openmpi.

I have attached the log file.

achyutan
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Old   February 12, 2013, 06:16
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Hi achyutan,

Start a new terminal and try running AllMake once again! I think the reason for MPI not being detected is due to a missing shell refresh.

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Old   February 13, 2013, 07:19
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Hi Bruno,

You are spot on. When I try to open a new terminal I get linked to the former session when I sourced the environment variables. I have attached a text file showing what I get while opening a new terminal.
so, when i run './AllMake' I still get the same errors during stage3.
Could you give me a solution for this ?

achyutan
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Old   February 13, 2013, 17:00
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Hi achyutan,

What does the following command output?
Code:
ls -l $HOME/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linuxGccDPOpt/bin
Best regards,
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Old   February 14, 2013, 06:33
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Hi Bruno,

I got the following when I gave ls- l inside /ThirdParty/packages/openmpi-1.4.3/platforms/linuxGccDPOpt/bin :

srinivasanraghavach@ubuntu:~/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linuxGccDPOpt/bin$ ls -l
total 0
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpic++ -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpicc -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpiCC -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpicc-vt -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpiCC-vt -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpic++-vt -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpicxx -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpicxx-vt -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 7 2013-02-06 20:18 mpiexec -> orterun
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpif77 -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpif77-vt -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpif90 -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 12 2013-02-06 20:18 mpif90-vt -> opal_wrapper
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 7 2013-02-06 20:18 mpirun -> orterun
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 10 2013-02-06 20:18 ompi-clean -> orte-clean
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 ompi_info
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 8 2013-02-06 20:18 ompi-iof -> orte-iof
lrwxrwxrwx 1 srinivasanraghavach srinivasanraghavach 7 2013-02-06 20:18 ompi-ps -> orte-ps
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 ompi-server
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 opal_wrapper
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 opari
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 orte-clean
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 orted
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 orte-iof
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 orte-ps
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 orterun
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 otfaux
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 otfconfig
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 otfdump
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 otfinfo
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 otfmerge
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 vtcc
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 vtcxx
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 vtfilter
-rwxr-xr-x 1 srinivasanraghavach srinivasanraghavach 0 2013-02-06 20:18 vtunify


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Old   February 15, 2013, 05:04
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Hi,

is there anyone who has recently had success in installing OF-1.6-ext on ubuntu natty (11.04) ?


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Old   February 15, 2013, 08:25
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Hi achyutan,

Sorry, didn't manage to answer you sooner.
OK, Open-MPI seems to be properly installed. Then check the following details:
  1. If the path for Open-MPI is in the PATH variable:
    Code:
    echo $PATH | grep "ThirdParty/packages/openmpi-1.4.3/platforms/linuxGccDPOpt/bin"
    It should output a long line of paths. If it does not, then something is broken somewhere.
  2. If the previous one is OK, then the next ones should also work:
    Code:
    which mpirun
    which mpicc
    If they do not work, then something has gone wrong somewhere...
Best regards,
Bruno
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Old   February 17, 2013, 06:46
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Hi Bruno,

yeah, you are right. It does not return any path. All those commands do not return anything.

As you said, I feel it could be due to shell refresh. Whenever I start a terminal, it starts with the former session showing the details of sourcing environment variables. Have you checked the file 'terminal.txt' ?

could it be due to shell not being refreshed ? If so, how to overcome it?

-achyutan
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Old   February 17, 2013, 08:05
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Hi achyutan,

This is very strange... what does the following file contain:
Code:
$HOME/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linuxGccDPOpt/etc/openmpi-1.4.3.sh
Note: whenever a new terminal is started, the environment is as good as refreshed.

Best regards,
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Old   February 20, 2013, 01:50
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Hi,

openmpi-1.4.3.sh file is empty ! and so is openmpi-1.4.3.csh. However, my shell is based on bash only and not csh.

-achyutan
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Old   February 20, 2013, 03:31
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Quick answer - it should have this inside:
Code:
# Load openmpi-1.4.3 libraries and binaries
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
export OPENMPI_DIR=$WM_THIRD_PARTY_DIR/packages/openmpi-1.4.3/platforms/$WM_OPTIONS
export OPENMPI_BIN_DIR=$OPENMPI_DIR/bin
export OPENMPI_LIB_DIR=$OPENMPI_DIR/lib

# Enable access to the package runtime applications and libraries
[ -d $OPENMPI_BIN_DIR ] && _foamAddPath $OPENMPI_BIN_DIR
[ -d $OPENMPI_LIB_DIR ] && _foamAddLib  $OPENMPI_LIB_DIR

export MPI_HOME=$OPENMPI_DIR
export MPI_ARCH_PATH=$MPI_HOME
export OPAL_PREFIX=$MPI_ARCH_PATH

# We initialize the rest of the environment using mpicc --showme:
export OPENMPI_INCLUDE_DIR="`mpicc --showme:incdirs`"
export OPENMPI_COMPILE_FLAGS="`mpicc --showme:compile`"
export OPENMPI_LINK_FLAGS="`mpicc --showme:link`"

# Set the OpenFOAM compilation flags 
export PINC=$OPENMPI_COMPILE_FLAGS
export PLIBS=$OPENMPI_LINK_FLAGS


if [ "$FOAM_VERBOSE" -a "$PS1" ]
then
    echo "  Environment variables defined for OpenMPI:"
    echo "    OPENMPI_BIN_DIR       : $OPENMPI_BIN_DIR"
    echo "    OPENMPI_LIB_DIR       : $OPENMPI_LIB_DIR"
    echo "    OPENMPI_INCLUDE_DIR   : $OPENMPI_INCLUDE_DIR"
    echo "    OPENMPI_COMPILE_FLAGS : $OPENMPI_COMPILE_FLAGS"
    echo "    OPENMPI_LINK_FLAGS    : $OPENMPI_LINK_FLAGS"
    echo ""
    echo "    MPI_HOME              : $MPI_HOME"
    echo "    MPI_ARCH_PATH         : $MPI_ARCH_PATH"
    echo "    OPAL_PREFIX           : $OPAL_PREFIX"
    echo "    PINC                  : $PINC"
    echo "    PLIBS                 : $PLIBS"
fi
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Old   February 21, 2013, 05:28
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Hi Bruno,

I tried downloading openmpi manually and put it inside ThirdPatry/sources and got the same error w.r.t openmpi.
openmpi-1.4.3.sh file is empty and i have no idea why so.
is there any other way out to install OF-1.6-ext ?
is it possible to install on mac os x lion?
Once, i tried installing OF 2.0.x from :http://http://www.optimulation.com/2...mac-os-x-lion/ on lion but did not succeed due to technical issues regarding macports.

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Old   February 21, 2013, 07:04
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Hi achyutan,

Have you tried editing the empty file and placing inside it the code I posted yesterday?

As for installing on Mac Lion: it should be possible and it should work, but I've never done it myself. I vaguely remember that there was a thread on that topic back when 1.6-ext was first released...

Best regards,
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Old   February 21, 2013, 09:40
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Hi Bruno,

sorry, i did not try that code earlier.
Now, I get different errors during stage 3 compilation of AllMake.
this time it is due to './dummysizes' command not found. I have attached the log file.
humble thanks for your suggestions and replies. I hope you can figure out the 'strange' problem which i am not able to.
I sourced the environment variables again after editing the openmpi.sh file. I get the follwing in the terminal :

Code:
~/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty$ source $HOME/.bashrc
Sourcing: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/etc/prefs.sh
Sourcing: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/etc/settings.sh
Using openmpi-1.4.3 from the ThirdParty package: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3
Sourcing: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linuxGccDPOpt/etc/openmpi-1.4.3.sh
  Environment variables defined for OpenMPI:
    OPENMPI_BIN_DIR       : /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linuxGccDPOpt/bin
    OPENMPI_LIB_DIR       : /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linuxGccDPOpt/lib
    OPENMPI_INCLUDE_DIR   : 
    OPENMPI_COMPILE_FLAGS : 
    OPENMPI_LINK_FLAGS    : 

    MPI_HOME              : /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linuxGccDPOpt
    MPI_ARCH_PATH         : /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linuxGccDPOpt
    OPAL_PREFIX           : /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linuxGccDPOpt
    PINC                  : 
    PLIBS                 : 
Sourcing: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/mesquite-2.1.2/platforms/linuxGccDPOpt/etc/mesquite-2.1.2.sh
    MESQUITE_DIR is initialized to: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/mesquite-2.1.2/platforms/linuxGccDPOpt
Sourcing: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/metis-5.0pre2/platforms/linuxGccDPOpt/etc/metis-5.0pre2.sh
    METIS_DIR is initialized to: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/metis-5.0pre2/platforms/linuxGccDPOpt
    PARMETIS_DIR is initialized to: 
Sourcing: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/ParMGridGen-1.0/platforms/linuxGccDPOpt/etc/ParMGridGen-1.0.sh
    PARMGRIDGEN_DIR is initialized to: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/ParMGridGen-1.0/platforms/linuxGccDPOpt
Sourcing: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/libccmio-2.6.1/platforms/linuxGccDPOpt/etc/libccmio-2.6.1.sh
    LIBCCMIO_DIR is initialized to: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/libccmio-2.6.1/platforms/linuxGccDPOpt
    SCOTCH_DIR is initialized to: 
Sourcing: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/cmake-2.8.8/platforms/linuxGccDPOpt/etc/cmake-2.8.8.sh
    CMAKE_DIR is initialized to: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/cmake-2.8.8/platforms/linuxGccDPOpt
    M4_DIR is initialized to: 
    BISON_DIR is initialized to: 
    FLEX_DIR is initialized to: 
    ZOLTAN_DIR is initialized to: 
    PYTHON_DIR is initialized to: 
    QT_DIR is initialized to: /usr
    PARAVIEW_DIR is initialized to: 
Sourcing: /home/srinivasanraghavach/OpenFOAM/OpenFOAM-1.6-ext/etc/aliases.sh
you can find there that parmetis is not being sourced and parmetis_dir is initialized to nothing. why so ?
-achyutan
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Old   February 21, 2013, 13:28
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Hi achyutan,

this is starting to look very suspicious... it's as if someone has removed vital files somehow and somewhere along the building process

My suggestion is to start over from a clean copy of 1.6-ext's source code. But keep a backup of the source packages you placed in the RPM source folder, and make sure that all of those files are not empty or incomplete in some way.

Best regards,
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Old   February 25, 2013, 08:55
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Hi Bruno,

I removed everything and tried again. It worked for me. no problems in stage 3 compilation of Thirdparty.
Now, a minor problem arises in stage 4. Not able to connect to : http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.7.4.tar.gz
even when i try to connect to the url manually. could you tell me how to get this package?

- achyutan
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