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Old   December 24, 2010, 06:18
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Giovanni Caramia
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I use opensuse 11.3 and I'm having a similar problem with AllMake.stage2. This is the end of the output:

make[1]: Leaving directory `/home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/openmpi-1.4.3'
+ echo ''

+ echo 'Generating OpenFOAM specific .csh and .sh files for the package openmpi-1.4.3'
Generating OpenFOAM specific .csh and .sh files for the package openmpi-1.4.3
+ echo ''

+ mkdir -p /home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64//home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/etc
+ cat
+ cat
+ /usr/lib/rpm/brp-lib64-linux
sf@suse.de: if you find problems with this script, drop me a note
+ RPM_BUILD_ROOT=/home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64
+ export RPM_BUILD_ROOT
+ test -x /usr/sbin/Check -a 1000 = 0 -o -x /usr/sbin/Check -a '!' -z /home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64
+ echo 'I call /usr/sbin/Check...'
I call /usr/sbin/Check...
+ /usr/sbin/Check
/home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/etc/settings.sh: line 67: /home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/etc/openmpi-1.4.3.sh: No such file or directory
errore: Stato d'uscita errato da /home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.1FRj0B (%install)


Errori di compilazione RPM:
Stato d'uscita errato da /home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.1FRj0B (%install)
Package openmpi-1.4.3 is already installed
Done installing package openmpi-1.4.3

========================================
Done ThirdParty AllMake: Stage2
========================================
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Old   January 6, 2011, 15:50
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This may look similar to the problems in the previous posts involving openmpi, but I think it is different.

I successfully installed 1.6-ext under openSUSE 11.1 by cloning the git repo and installing the ThirdParty libraries using the AllMake script. Everything seemed to go okay with openmpi, and I'm able to run the interFoam/laminar/damBreak case in parallel, for example; however, a problem arises when I try to link a separate executable of my own with the openmpi libraries.

I compile my executable using Autotools and a configure command that includes the command line option --with-mpi=$MPI_ARCH_PATH, where MPI_ARCH_PATH is /mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt. During the linking process I get these errors:
Code:
libtool: link: warning: library `/mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/libmpi.la' was moved.
/usr/bin/grep: /mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/openmpi-1.4.3-root/mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/libopen-rte.la: No such file or directory
/usr/bin/sed: can't read /mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/openmpi-1.4.3-root/mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/libopen-rte.la: No such file or directory
libtool: link: `/mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/openmpi-1.4.3-root/mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/libopen-rte.la' is not a valid libtool archive
I can eliminate the first ("was moved") error by modifying the libdir variable in the $OPENMPI_DIR/lib/*.la files, but doing so does not alter the rest of the errors:
Code:
/usr/bin/grep: /mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/openmpi-1.4.3-root/mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/libopen-rte.la: No such file or directory
/usr/bin/sed: can't read /mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/openmpi-1.4.3-root/mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/libopen-rte.la: No such file or directory
libtool: link: `/mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/openmpi-1.4.3-root/mnt/disk4/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/libopen-rte.la' is not a valid libtool archive
It looks to me like the *rpmBuild/BUILD/openmpi* path, which existed only temporarily when the package was first built, is present within the mpicxx executable, which I assume is the problem.

... So ... any ideas on how to get out of this? The README.ThirdParty discusses relocating the RPM root installation directory. Do I need to re-install from the RPM following that advice (i.e. even though openmpi seems to otherwise be "working" now)?

Thanks,
David
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Old   January 6, 2011, 18:35
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Hello David,

Would you mind sending me a little autotools/automake preconfigured test case, where the main program simply calls MPI_Init() and then exits?

That way, I could rapidly test this problem when trying to link with the openmpi libraries installed under the 1.6-ext Third Party Pack.

Martin
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Old   January 6, 2011, 22:46
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Martin- Thanks. That sounds great. I'll work on putting something together.
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Old   January 15, 2011, 18:07
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Mathieu Olivier
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Dear Martin,

I had an issue while compiling the ThirdParty package using the system openmpi (on ubuntu 10.04). The compilation of scotch complains about a missing mpi.h file...

Changing the line 42 in the "scotch-5.1.10b_patch_0" file :

+CCD = gcc -I$(MPI_HOME)/include

by either

+CCD = gcc -I$(MPI_HOME)/include/mpi

or

+CCD = gcc -I$(OPENMPI_INCLUDE_DIR)

solved the problem. Just to let you know...

Regards,

Mathieu
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Old   January 15, 2011, 18:10
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Quote:
I had an issue while compiling the ThirdParty package using the system openmpi (on ubuntu 10.04). The compilation of scotch complains about a missing mpi.h file...
Actually, there is an SYSTEMOPENMPI option, which excatly written for this issue, but I am afraid people do not notice it very often.
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Old   January 15, 2011, 18:25
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Mathieu Olivier
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Dear Daniel,

I actually use the SYSTEMOPENMPI option in my prefs.sh file :

export WM_MPLIB=SYSTEMOPENMPI

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Old   January 15, 2011, 18:33
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Really, that's quite strange.. You see, you said when you set

Quote:
+CCD = gcc -I$(OPENMPI_INCLUDE_DIR)
solved the problem
And also, see in etc/settings.sh SYSTEMOPENMPI) block,

there are lines
Quote:
[ ! -n "${OPENMPI_INCLUDE_DIR}" ] && export OPENMPI_INCLUDE_DIR="`mpicc --showme:incdirs`"
[ ! -n "${OPENMPI_COMPILE_FLAGS}" ] && export OPENMPI_COMPILE_FLAGS="`mpicc --showme:compile`"
[ ! -n "${OPENMPI_LINK_FLAGS}" ] && export OPENMPI_LINK_FLAGS="`mpicc --showme:link`"

#
# WARNING: We assume the file mpi.h will be available under the directories identified
# by the variable $OPENMPI_INCLUDE_DIR. Otherwise, please double check your
# system openmpi installation.
I think these lines are trying to automatically find where the system mpi.h file by using
Quote:
`mpicc --showme:incdirs`
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Old   January 15, 2011, 18:48
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Well, it seams that the compiler only sees $MPI_HOME (+CCD = gcc -I$(MPI_HOME)/include) which points to /usr/include on my system. And since the link to the system openmpi include directory is /usr/include/mpi on ubuntu 10.04, I need to modify the "scotch-5.1.10b_patch_0" file... unless I am missing something else...
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Old   January 15, 2011, 18:56
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Oh, I see. Thanks for explanation. I always check the building time of every parts, and I found, openmpi usally does not take very long time, it is quite fast now, it is paraview and openfoam are the real big monsters. Since then, I start to use NOT the system openmpi.

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Old   January 16, 2011, 19:02
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Quote:
Originally Posted by mathieu View Post
Dear Martin,

I had an issue while compiling the ThirdParty package using the system openmpi (on ubuntu 10.04). The compilation of scotch complains about a missing mpi.h file...

Changing the line 42 in the "scotch-5.1.10b_patch_0" file :

+CCD = gcc -I$(MPI_HOME)/include

by either

+CCD = gcc -I$(MPI_HOME)/include/mpi

or

+CCD = gcc -I$(OPENMPI_INCLUDE_DIR)

solved the problem. Just to let you know...

Regards,

Mathieu
After further tests, I realized that the second correction I proposed earlier does not work. So, just to be clear, I replaced the line

+CCD = gcc -I$(MPI_HOME)/include

by

+CCD = gcc -I$(MPI_HOME)/include/mpi

and the compilation of scotch worked.

Mathieu
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Old   January 21, 2011, 17:24
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There have been no replies or suggestions regarding 'karamiag' and 'ashishnedungadi' issues with openmpi error during stage 2. I want to add my name to the list of people with the same issue.

All the output from stage 2 in a log file exceeds the upload size limits for the forums so here's the last 20 lines with error:

Code:
...
/opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib/libopen-rte.la:libdir='/opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64/opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/lib'
Found '/opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64' in installed files; aborting
error: Bad exit status from /opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.abfac7 (%install)


RPM build errors:
    Bad exit status from /opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.abfac7 (%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: /opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/openmpi-1.4.3-linux64GccDPOpt.x86_64.rpm
error: open of /opt/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

========================================
Done ThirdParty AllMake: Stage2
========================================
I am running RHEL 6.0 x86_64. Let me know if there's any other information I need/should supply to help track this down.
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Old   January 22, 2011, 07:01
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Hi Chris,
I hope this help: abaut my last post, I think the problem is in the command

+ mkdir -p/home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64//home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/etc
where /home is repeated twice, so this command creates directories in the wrong path. I tried to fix this but with no success.
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Old   January 28, 2011, 09:56
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New machine, new problem. When installing from an rpm (specifically for openmpi, although I suspect the same will be true for any rpm), I get this error:
Code:
error: can't create transaction lock on /var/lock/rpm/transaction
Some notes:
  • I do not have root access on the machine (but don't expect I need it).
  • The /var/lock/rpm directory exists (for better or worse) with user and group name both "rpm" and with drwxr-xr-x access. The problem exists whether or not there is already a file in that directory called "transaction".
  • Red Hat Enterprise Linux WS release 4 (Nahant Update 6)
  • Typing the command "rpm -ivhvv <path/file.rpm> --dbpath <path/rpmDB> --force --nodeps" as gathered from the script, reproduces the error directly.
I've looked around for a solution to such problems but haven't even come up with a consensus on whether or not it indicates that I need root privileges, so I'd be grateful for any suggestions.

Thanks,
David
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Old   January 28, 2011, 10:13
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I found this a while back:

http://www.nordugrid.org/documents/r...everybody.html

Although I don't know if OF-1.6-ext will work.
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Old   January 28, 2011, 11:16
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Thanks Laurence. That's a very helpful link but unfortunately does not mention transaction locks. Every mention I can find of transaction locks is solved by someone saying "oh, I forgot to be root", but I thought the plan here was not to require that. Plus, I have already installed successfully on two other machines (with different OS) where I was not root.
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Old   January 28, 2011, 11:25
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I see. Does this help? Otherwise I'm stuck.

https://www.redhat.com/archives/rpm-.../msg00048.html
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Old   January 28, 2011, 11:40
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Yes- I think that does help! On the machine where I am unable to install, the lock path is hardwired to /var/lock/rpm/transaction, whereas on the machine where I am able to install, it is set to %{_dbpath}/__db.000. Since the install command specifies a local dbpath, and it's not being used to define the lock path, I'm guessing that's the problem. I'll let you know once I get some help changing it.

Thanks!
David
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Old   January 28, 2011, 12:50
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For the record, changing the rpm lock path fixed the problem. I subsequently ran into another error (discussed here) - removing the __db* files from the local rpm database appeared to resolve that problem.

Thanks Laurence!
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Old   February 2, 2011, 20:37
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Quote:
Originally Posted by karamiag View Post
Hi Chris,
I hope this help: abaut my last post, I think the problem is in the command

+ mkdir -p/home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64//home/tecnici/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/openmpi-1.4.3/platforms/linux64GccDPOpt/etc
where /home is repeated twice, so this command creates directories in the wrong path. I tried to fix this but with no success.
Giovanni, I've sifted through the build scripts and I believe the paths its creating/using are fine (it appears to be duplicating the path twice but it's actually not - it does it intentionally).

From what I've found it seems to build the openmpi binaries and libraries in the BUILDROOT dir Ok but fails to create the .rpm file. Hence the 'open' error in my last post.

I'm going to dig around more to see why it did not make the rpm but it wasn't obvious in the AllMake.stage2 output. Maybe at this point I will direct my inquiry toward Martin Beaudoin (the author of the build system) ... Martin, you have some hints about determining why the rpm wouldn't get built?
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