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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
Attached Files
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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File Type: gz log1.tar.gz (5.2 KB, 3 views)
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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,
Bruno
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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.

Best regards,
Bruno
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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,
Bruno
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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) ?


achyutan
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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,
Bruno
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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.

-achyutan
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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,
Bruno
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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,
Bruno
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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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