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Old   December 8, 2010, 11:52
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  #41
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Guilherme da Silva
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I am using Ubuntu 10.04 and I had to make two changes to compile the ThirdParty tools:

1) before compiling AllMake.stage4 (Paraview):

Quote:
export QT_DIR=/usr
2) before compiling AllMake.stage3:

Quote:
sudo ln -s /usr/bin/make /usr/bin/gmake
But now I can still can not compile Paraview and the main code...a lot of errors...

ThirdParty - 0,1,2,3 passed but 4 not (this is not a problem because I do have other paraview installation)
src/Allwmake - passed OK
applications/Allwmake - crashed!

Quote:
/home/ats4i/OpenFOAM/ats4i-1.6-ext/lib/linux64GccDPOpt/libscotchDecomp.so: undefined reference to `Foam::OFstream::OFstream(Foam::fileName const&, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber, Foam::IOstream::compressionType)'

Last edited by aerothermal; December 8, 2010 at 12:06. Reason: addition
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Old   December 8, 2010, 12:09
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I wonder whether your "scotch" really compiled successfully. Mine failed under ubuntu 10.04 because /usr/lib/libz.a was missing, which was repaired by

Code:
sudo apt-get install zlib1g-dev
Quote:
Originally Posted by aerothermal View Post
I am using Ubuntu 10.04 and I had to make two changes to compile the ThirdParty tools:

1) before compiling AllMake.stage4 (Paraview):



2) before compiling AllMake.stage3:



But now I can still can not compile Paraview and the main code...a lot of errors...

ThirdParty - 0,1,2,3 passed but 4 not (this is not a problem because I do have other paraview installation)
src/Allwmake - passed OK
applications/Allwmake - crashed!
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Old   December 8, 2010, 12:12
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Guilherme da Silva
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Hi Boger,

Yes I do have the zlib1g-dev in newest version.

See that stage 3 appears to be fine...

Quote:
========================================
Starting ThirdParty AllMake: Stage3
========================================

Updating the ThirdParty environment variables before building package metis-5.0pre2
Package metis-5.0pre2 is already installed
Done installing package metis-5.0pre2

Updating the ThirdParty environment variables before building package ParMGridGen-1.0
Package ParMGridGen-1.0 is already installed
Done installing package ParMGridGen-1.0

Updating the ThirdParty environment variables before building package mesquite-2.1.2
Package mesquite-2.1.2 is already installed
Done installing package mesquite-2.1.2

Updating the ThirdParty environment variables before building package scotch-5.1.10b
Package scotch-5.1.10b is already installed
Done installing package scotch-5.1.10b

Updating the ThirdParty environment variables before building package ParMetis-3.1.1
Package ParMetis-3.1.1 is already installed
Done installing package ParMetis-3.1.1

========================================
Done ThirdParty AllMake: Stage3
========================================
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Old   December 9, 2010, 13:14
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I am running Fedora Core 13, 64-bit and I was not making any progress with compiling 1.6-ext. I found out I don't have the executable rpmbuild. So, I had to install it using instructions found here:

http://www.g-loaded.eu/2006/04/05/ho...ges-on-fedora/

Now I have rpmbuild and the install is much happier. Still have a ways to go, but I will report back if everthing goes smoothly.

@Martin: Apparently rpmbuild is not standard, so a good check would be to see if rpmbuild exists. Thanks for all your hard work on this project.
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Old   December 9, 2010, 13:33
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Similarly, under ubuntu 10.04, I found I needed

Code:
sudo apt-get install bison flex build-essential git gitk git-gui rpm
plus

Code:
sudo apt-get install libxt-dev
for ParaView-3.8.1/VTK (to pick up X11/StringDefs.h and X11/Intrinsic.h) in AllMake.stage4,

Code:
sudo apt-get install zlib1g-dev
for scotch-5.1.10b in AllMake.stage3,

Code:
sudo apt-get install gnuplot python-numpy
for pyFoam,

Code:
sudo apt-get install binutils-dev
to get libiberty for the applications Allwmake, and

Code:
sudo apt-get install libtool autoconf
for components in the Turbomachinery breeder package.

I also needed to link make to gmake for ParMGridGen-1.0, as mentioned above.

Maybe all of this could have been avoided when the OS was installed...
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Old   December 9, 2010, 13:37
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I have all those libraries in Ubuntu 10.04 but the code still does not compile.
see error above...
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Old   December 9, 2010, 13:52
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Can you post a little more of the log file preceding your applications error message (e.g. what application was compiling and what was its compile command)?

Also, why is libscotchDecomp in the user-ext-1.6/lib? I imagine you would have had to override the usual setting for WM_PROJECT_DIR?
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Old   December 9, 2010, 14:03
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ThirdParty/AllMake.stage4

Quote:
Qt QTGUI library not found.
Qt QTSQL library not found.
Qt QTNETWORK library not found.
Qt QTCORE library not found.
CMake Error at VTK/GUISupport/Qt/CMakeLists.txt:123 (QT4_WRAP_CPP):
Unknown CMake command "QT4_WRAP_CPP".


-- Configuring incomplete, errors occurred!
error: Bad exit status from /home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.WNiFnF (%build)


RPM build errors:
Bad exit status from /home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.WNiFnF (%build)
Installing package: ParaView-3.8.1
Uninstalling ParaView-3.8.1 using RPM: ParaView-3.8.1-linux64GccDPOpt.x86_64
Installing ParaView-3.8.1 using RPM file: /home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/ParaView-3.8.1-linux64GccDPOpt.x86_64.rpm
error: open of /home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/ParaView-3.8.1-linux64GccDPOpt.x86_64.rpm failed: No such file or directory
Done installing package ParaView-3.8.1
Allwmake

Quote:
~/OpenFOAM/OpenFOAM-1.6-ext$ ./Allwmake
+ wmake all solvers
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-40 -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/POD/lnInclude -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/finiteVolume/lnInclude -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/ODE/lnInclude -IlnInclude -I. -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/OpenFOAM/lnInclude -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/OSspecific/POSIX/lnInclude -fPIC Make/linux64GccDPOpt/PODSolver.o -L/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt \
-lfiniteVolume -lODE -lPOD -lOpenFOAM -liberty -ldl -lm -o /home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/PODSolver
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-40 -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/finiteVolume/lnInclude -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/randomProcesses/lnInclude -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/sampling/lnInclude -IlnInclude -I. -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/OpenFOAM/lnInclude -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/OSspecific/POSIX/lnInclude -fPIC Make/linux64GccDPOpt/dnsFoam.o -L/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt \
-lfiniteVolume -lrandomProcesses -lsampling -lmeshTools -lOpenFOAM -liberty -ldl -lm -o /home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/dnsFoam
/home/ats4i/OpenFOAM/ats4i-1.6-ext/lib/linux64GccDPOpt/libscotchDecomp.so: undefined reference to `Foam::OFstream::OFstream(Foam::fileName const&, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber, Foam::IOstream::compressionType)'
collect2: ld returned 1 exit status
make[2]: *** [/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/PODSolver] Error 1
make[1]: *** [PODSolver] Error 2
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-40 -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/finiteVolume/lnInclude -IlnInclude -I. -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/OpenFOAM/lnInclude -I/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/src/OSspecific/POSIX/lnInclude -fPIC Make/linux64GccDPOpt/laplacianFoam.o -L/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt \
-lfiniteVolume -llduSolvers -lOpenFOAM -liberty -ldl -lm -o /home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/laplacianFoam
/home/ats4i/OpenFOAM/ats4i-1.6-ext/lib/linux64GccDPOpt/libscotchDecomp.so: undefined reference to `Foam::OFstream::OFstream(Foam::fileName const&, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber, Foam::IOstream::compressionType)'
collect2: ld returned 1 exit status
make[2]: *** [/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/dnsFoam] Error 1
make[1]: *** [dnsFoam] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [DNS] Error 2
/home/ats4i/OpenFOAM/ats4i-1.6-ext/lib/linux64GccDPOpt/libscotchDecomp.so: undefined reference to `Foam::OFstream::OFstream(Foam::fileName const&, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber, Foam::IOstream::compressionType)'
collect2: ld returned 1 exit status
make[2]: *** [/home/ats4i/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/laplacianFoam] Error 1
make[1]: *** [laplacianFoam] Error 2
I have 1.7 and 1.5dev versions in home/user/OpenFoam directory.
the bashrc for each version is sourced by the user in order to choose the version.

Last edited by aerothermal; December 9, 2010 at 14:26. Reason: typo
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Old   December 9, 2010, 17:06
Default Problems with Stage 2-openmpi1.4.3
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Ashish Nedungadi
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On FC13, 64-bit, I am still having problems with Stage 2, which is the openmpi-1.4.3 step. Here are some of the errors I get at the very end:

+ /usr/lib/rpm/check-rpaths /usr/lib/rpm/check-buildroot
************************************************** *****************************
*
* WARNING: 'check-rpaths' detected a broken RPATH and will cause 'rpmbuild'
* to fail. To ignore these errors, you can set the '$QA_RPATHS'
* environment variable which is a bitmask allowing the values
* below. The current value of QA_RPATHS is 0x0000.
*
* 0x0001 ... standard RPATHs (e.g. /usr/lib); such RPATHs are a minor
* issue but are introducing redundant searchpaths without
* providing a benefit. They can also cause errors in multilib
* environments.
* 0x0002 ... invalid RPATHs; these are RPATHs which are neither absolute
* nor relative filenames and can therefore be a SECURITY risk
* 0x0004 ... insecure RPATHs; these are relative RPATHs which are a
* SECURITY risk
* 0x0008 ... the special '$ORIGIN' RPATHs are appearing after other
* RPATHs; this is just a minor issue but usually unwanted
* 0x0010 ... the RPATH is empty; there is no reason for such RPATHs
* and they cause unneeded work while loading libraries
* 0x0020 ... an RPATH references '..' of an absolute path; this will break
* the functionality when the path before '..' is a symlink
*
*
* Examples:
* - to ignore standard and empty RPATHs, execute 'rpmbuild' like
* $ QA_RPATHS=$[ 0x0001|0x0010 ] rpmbuild my-package.src.rpm
* - to check existing files, set $RPM_BUILD_ROOT and execute check-rpaths like
* $ RPM_BUILD_ROOT=<top-dir> /usr/lib/rpm/check-rpaths
*
************************************************** *****************************
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/bin/ompi-server' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/bin/orted' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/bin/opal_wrapper' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/bin/orte-iof' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/bin/orte-ps' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/bin/ompi_info' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/bin/orte-clean' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/bin/orterun' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
************************************************** *****************************
*
* WARNING: 'check-rpaths' detected a broken RPATH and will cause 'rpmbuild'
* to fail. To ignore these errors, you can set the '$QA_RPATHS'
* environment variable which is a bitmask allowing the values
* below. The current value of QA_RPATHS is 0x0000.
*
* 0x0001 ... standard RPATHs (e.g. /usr/lib); such RPATHs are a minor
* issue but are introducing redundant searchpaths without
* providing a benefit. They can also cause errors in multilib
* environments.
* 0x0002 ... invalid RPATHs; these are RPATHs which are neither absolute
* nor relative filenames and can therefore be a SECURITY risk
* 0x0004 ... insecure RPATHs; these are relative RPATHs which are a
* SECURITY risk
* 0x0008 ... the special '$ORIGIN' RPATHs are appearing after other
* RPATHs; this is just a minor issue but usually unwanted
* 0x0010 ... the RPATH is empty; there is no reason for such RPATHs
* and they cause unneeded work while loading libraries
* 0x0020 ... an RPATH references '..' of an absolute path; this will break
* the functionality when the path before '..' is a symlink
*
*
* Examples:
* - to ignore standard and empty RPATHs, execute 'rpmbuild' like
* $ QA_RPATHS=$[ 0x0001|0x0010 ] rpmbuild my-package.src.rpm
* - to check existing files, set $RPM_BUILD_ROOT and execute check-rpaths like
* $ RPM_BUILD_ROOT=<top-dir> /usr/lib/rpm/check-rpaths
*
************************************************** *****************************
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/libopen-rte.so.0.0.0' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/libmpi.so.0.0.2' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/openmpi/mca_mpool_sm.so' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/openmpi/mca_btl_sm.so' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
ERROR 0002: file '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/openmpi/mca_coll_sm.so' contains an invalid rpath '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib' in [/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib]
error: Bad exit status from /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.DZR2Yx (%install)


RPM build errors:
Bad exit status from /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.DZR2Yx (%install)
Installing package: openmpi-1.4.3
Uninstalling openmpi-1.4.3 using RPM: openmpi-1.4.3-linux64GccDPOpt.x86_64
Installing openmpi-1.4.3 using RPM file: /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/openmpi-1.4.3-linux64GccDPOpt.x86_64.rpm
error: open of /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/openmpi-1.4.3-linux64GccDPOpt.x86_64.rpm failed: No such file or directory
Done installing package openmpi-1.4.3


Anybody else compiling on Fedora Core 13 64-bit system? Any help would be appreciated. Thanks!

Ashish
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Old   December 9, 2010, 17:21
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Dear Boger,

I managed to compile Paraview. See the other forum about QT. Actually I have qt3 and qt4 in system so I had to configure that to qt4.

But regarding directories I have:

Quote:
$ echo $WM_PROJECT
OpenFOAM
$ echo $WM_PROJECT_DIR
$HOME/OpenFOAM/OpenFOAM-1.6-ext
But I had recompiled Scotch by some reason that I could not remember in the user directory. This caused conflict between the undesirable surrogate $WM_USER_DIR/lib/linux64GccDPOpt and the actual library in 1.6ext distribution.

After I deleted the surrogate, the 1.6ext compiled properly.

Thank you boger for the light on this.

Regards,

Guilherme

Last edited by aerothermal; December 10, 2010 at 06:27. Reason: fixed issue
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Old   December 9, 2010, 22:13
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> @Martin: Apparently rpmbuild is not standard, so a good check would be to see if rpmbuild exists.

I just put a note in the ThirdParty/README file about 'rpm' and 'rpmbuild' being prerequisite applications in order to compile the ThirdParty packs.

In the early design of the new ThirdParty compilation process, I thought about supplying 'rpm' as an optional ThirdParty package too.

A simple bash script to download and compile rpm/rpmbuild as a bootstrap step for the whole ThirdParty compilation process would have been provided.

I thought it was a tad overkill, but if installing rpm/rpmbuild on most systems turns out to be a difficult step, maybe supplying a way to compile and install rpm/rpmbuild from source code would be useful after all.

Martin

Quote:
Originally Posted by ashishnedungadi View Post
I am running Fedora Core 13, 64-bit and I was not making any progress with compiling 1.6-ext. I found out I don't have the executable rpmbuild. So, I had to install it using instructions found here:

http://www.g-loaded.eu/2006/04/05/ho...ges-on-fedora/

Now I have rpmbuild and the install is much happier. Still have a ways to go, but I will report back if everthing goes smoothly.

@Martin: Apparently rpmbuild is not standard, so a good check would be to see if rpmbuild exists. Thanks for all your hard work on this project.
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Old   December 10, 2010, 01:56
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Hello,

A Good Morning to everyone!

On Fedora, in order to get all the OpenFOAM-1.6-ext Third Party packages to build fine using the RPM approach, I had to make some changes to the ".rpmmacros" file found in the user's home directory (/home/username/.rpmmacros)

My file currently looks like this:

%_topdir /mnt/Ego_01/applications/rpmbuild
%_smp_mflags %([ -z "$RPM_BUILD_NCPUS" ] \\\
&& RPM_BUILD_NCPUS="`/usr/bin/getconf _NPROCESSORS_ONLN`"; \\\
if [ "$RPM_BUILD_NCPUS" -gt 16 ]; then echo "-j16"; \\\
elif [ "$RPM_BUILD_NCPUS" -gt 3 ]; then echo "-j$RPM_BUILD_NCPUS"; \\\
else echo "-j3"; fi)
%__arch_install_post # /usr/lib/rpm/check-rpaths /usr/lib/rpm/check-buildroot

in the last line, as can be seen, I have commented out everything after the "%__arch_instal_post" command.

If I remember right, it is also ok to comment out the entire line.... it would then look like:
# %__arch_install_post /usr/lib/rpm/check-rpaths /usr/lib/rpm/check-buildroot

Some of the errors I saw posted on this thread are directly connected with the "rpaths" and the "buildroot" checks which Fedora recommends, but causes issues when creating relocatable and locally installed rpms....

Disabling these two checks have NOT caused any other problems on my system so far..... everything seems to work fine :-)!

For information... my system is: Fedora 14 (32-bit)

P.S 1: Installing "rpmbuild" on Fedora is merely a question of running:
yum install rpm-build
yum install rpmdevtools
rpmdev-setuptree

Nothing complicated about that :-)!

P.S 2: Currently, in order to get OF-1.6-ext compiled properly on Fedora versions >13, you need to make a change in the wmake rules.... I have submitted a bug (and bug-fix suggestion) on the OF-1.6-ext bugtracker.... check out issue number 40 (http://sourceforge.net/apps/mantisbt..._view_page.php)

Hope this helps....

Philippose
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Old   December 11, 2010, 10:14
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Hi, Philippose,

I am usnig OpenSUSE 11.3. I do not have .rpmmacros. Is it normal? Do I need to create this manually?

Thanks!

Pei
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Old   December 11, 2010, 11:07
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Hello,

No you DON'T need a .rpmmacros file for compiling the ThirdParty packages of OF-1.6-ext.

I've NEVER used such a file myself, on all the Unix distros I have been using for designing and testing this new compilation process for the ThirdParty pack, including Fedora.

If you DO happen to have a .rpmmacros file because you've built RPM packages before, THEN checking it out like Philippose did might be helpful.

As for Philippose additional instructions to get rpm/rpmbuild to compile packages in parallel using "make -j number_of_procs", this is no longer necessary.
I have contributed fixes to the git repository in order to do that directly within the .spec files by using the good old environment variable $WM_NCOMPPROCS when compiling packages with 'make'. Those modifications will get merge into the master branch in due time.

Again, the RPM based compilation of the ThirdParty packages was designed to be self contained as much as possible. All the necessary operations are within the ThirdParty packages compilation bash scripts and in the various package's .spec files.

The only thing missing is the complementary development packages that you will need to install, like rpm/rpmbuild, flex/bison, some -dev libraries, mainly because many of todays Linux distros are not configured by default to do software development right off the bat.

Martin

Quote:
Originally Posted by phsieh2005 View Post
Hi, Philippose,

I am usnig OpenSUSE 11.3. I do not have .rpmmacros. Is it normal? Do I need to create this manually?

Thanks!

Pei
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Old   December 11, 2010, 15:50
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Hello Martin,

As is usually the case, you are right :-)! You do not necessarily need the ".rpmmacros" file in order to create the ThirdParty RPMs, and neither do you need the commands in the rpmmacros file in order to obtain a parallel compilation.

I saw the changes you had made in the spec files a while ago.

Just that, in my system I happened to have a ".rpmmacros" file, which ended up causing conflicts and errors such as the RPATHS and the Build Root ones.

I am not sure (do not have my laptop this weekend), but maybe "rpmdev-setuptree" creates a ".rpmmacros" file..... can someone confirm this?

However the point is... maybe the rpmbuild system on different distributions handle these options differently, and maybe there is a default global configuration somewhere which adds on these tests by default unless explicitly overridden by a user-level configuration or something.

I wish you a great weekend ahead!

Philippose
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Old   December 23, 2010, 03:38
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Is there any news on this? I have the same problem here. I'm on SUSE Enterprise Linux 11. (git pulled on 23-12-2010)

Then another strange thing happened during the compilation. I manually had to add a lot of environment variables, since many header files could not be found. These were:

export SCOTCH_LIB_DIR=$SCOTCH_DIR/lib
export SCOTCH_INCLUDE_DIR=$SCOTCH_DIR/include

These variables LIB and INCLUDE had to be defined for: SCOTCH, METIS, PARMETIS, MESQUITE, OPENMPI

Also export QT_BIN_DIR=/usr/bin was required.

Best regards,
Alex


Quote:
Originally Posted by mbeaudoin View Post
Hello David,

This is a nagging little problem. I though we nailed it down properly with the fix contributed by Philippose, but it looks like we need to revisit this one yet again.

Basically, all the configuration parameters for compiling Mesquite were recommended by Sandeep Menon, so I basically applied the same recipe.

I don't mind changing the configure parameters as long as the compiled mesquite library is still usable by OF-1.6-ext. I will contact Sandeep in order to get some advices over this one.

In the meantime, would you mind telling me on what platform/OS you are experiencing this problem? I am having a very hard time replicating this problem, and I am using 6 different Unix flavours for testing the new ThirdParty packages setup, to no avail...

Thank you for your input!

Martin

Last edited by aloeven; December 23, 2010 at 05:29.
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Old   December 23, 2010, 04:22
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When I tried to run a case in parallel I got the error:
[machine:18193] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 125
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
orte_init:startup:internal-failure
But I couldn't open the help file:
$FOAM_INST_DIR/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/openmpi-1.4.3-root$FOAM_INST_DIR/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/share/openmpi/help-orte-runtime: No such file or directory. Sorry!
--------------------------------------------------------------------------
[machine:18193] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 543


After some searching, it was solved by defining:
export OPAL_PREFIX=$MPI_ARCH_PATH

Alex.

OpenFOAM-1.6-ext on SUSE Enterprise Linux 11 (patch level 1)

Last edited by aloeven; December 23, 2010 at 05:29.
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Old   December 23, 2010, 10:22
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Alex-

Re your question "Is there any news on this?", are you referring to the mesquite headers problems preventing OpenFOAM libraries from compiling? If so, the problem was resolved over the next several posts following the one you quoted.

As far as the LIB and INCLUDE paths, you should not have to set them yourself. If you look in settings.sh or settings.csh, you'll see them being set. These scripts are invoked by etc/cshrc or etc/bashrc. Did you source those files at the appropriate points after installing the packages? Looking at the settings.* file, you'll also see several conditions that need to be met for the paths to be set -- basically, certain versions of the packages are expected to be installed in certain places.
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Old   December 23, 2010, 10:37
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Hi David,

I have installed 1.6-ext on two distributions and on Fedora there is no problem. On the SUSE enterprise I see the problems mentioned in my post.

I will go throuh the bashrc, settings.sh and the posts again to see if I can locate the problem.

Alex.
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Old   December 23, 2010, 14:37
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So, I was having trouble getting past Stage 2 (openmpi-1.4.3 compile). Looking at some of the detail logs, I find this:

*** Initialization, setup
configure: builddir: /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/openmpi-1.4.3
configure: srcdir: /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/openmpi-1.4.3
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
installing to directory "/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt"

Take a look at the "installing to directory". It's all mangled up and it throws off the installation of openmpi. At the very end I get these errors:

Found '/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64' in installed files; aborting
error: Bad exit status from /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.50EA0c (%install)


RPM build errors:
Bad exit status from /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.50EA0c (%install)
Installing package: openmpi-1.4.3
Uninstalling openmpi-1.4.3 using RPM: openmpi-1.4.3-linux64GccDPOpt.x86_64
Installing openmpi-1.4.3 using RPM file: /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/openmpi-1.4.3-linux64GccDPOpt.x86_64.rpm
error: open of /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/openmpi-1.4.3-linux64GccDPOpt.x86_64.rpm failed: No such file or directory
Done installing package openmpi-1.4.3

The way I got around this was to move /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3 to /home/neduna1/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages

Anybody else seeing this?
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