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#61 |
Member
Giovanni Caramia
Join Date: Mar 2009
Location: Bari, ITALY
Posts: 58
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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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#62 |
Senior Member
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
Rep Power: 17 ![]() |
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 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 ... 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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David A. Boger |
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#63 |
Senior Member
Martin Beaudoin
Join Date: Mar 2009
Posts: 332
Rep Power: 22 ![]() |
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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#64 |
Senior Member
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
Rep Power: 17 ![]() |
Martin- Thanks. That sounds great. I'll work on putting something together.
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David A. Boger |
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#65 |
Member
Mathieu Olivier
Join Date: Mar 2009
Location: Quebec City, Canada
Posts: 77
Rep Power: 17 ![]() |
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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#66 | |
Senior Member
Daniel WEI (老魏)
Join Date: Mar 2009
Location: Beijing, China
Posts: 689
Blog Entries: 9
Rep Power: 21 ![]() |
Quote:
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~ Daniel WEI ------------- Boeing Research & Technology - China Beijing, China |
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#67 |
Member
Mathieu Olivier
Join Date: Mar 2009
Location: Quebec City, Canada
Posts: 77
Rep Power: 17 ![]() |
Dear Daniel,
I actually use the SYSTEMOPENMPI option in my prefs.sh file : export WM_MPLIB=SYSTEMOPENMPI Mathieu |
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#68 | |||
Senior Member
Daniel WEI (老魏)
Join Date: Mar 2009
Location: Beijing, China
Posts: 689
Blog Entries: 9
Rep Power: 21 ![]() |
Really, that's quite strange.. You see, you said when you set
Quote:
there are lines Quote:
Quote:
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~ Daniel WEI ------------- Boeing Research & Technology - China Beijing, China |
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#69 |
Member
Mathieu Olivier
Join Date: Mar 2009
Location: Quebec City, Canada
Posts: 77
Rep Power: 17 ![]() |
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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#70 |
Senior Member
Daniel WEI (老魏)
Join Date: Mar 2009
Location: Beijing, China
Posts: 689
Blog Entries: 9
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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.
Regards,
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~ Daniel WEI ------------- Boeing Research & Technology - China Beijing, China |
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#71 | |
Member
Mathieu Olivier
Join Date: Mar 2009
Location: Quebec City, Canada
Posts: 77
Rep Power: 17 ![]() |
Quote:
+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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#72 |
Senior Member
Chris Sideroff
Join Date: Mar 2009
Location: Ottawa, ON, CAN
Posts: 434
Rep Power: 22 ![]() |
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 ======================================== |
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#73 |
Member
Giovanni Caramia
Join Date: Mar 2009
Location: Bari, ITALY
Posts: 58
Rep Power: 17 ![]() |
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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#74 |
Senior Member
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
Rep Power: 17 ![]() |
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
Thanks, David
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David A. Boger |
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#75 |
Senior Member
Laurence R. McGlashan
Join Date: Mar 2009
Posts: 370
Rep Power: 23 ![]() |
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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Laurence R. McGlashan :: Website |
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#76 |
Senior Member
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
Rep Power: 17 ![]() |
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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David A. Boger |
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#78 |
Senior Member
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
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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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David A. Boger |
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#79 |
Senior Member
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
Rep Power: 17 ![]() |
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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David A. Boger |
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#80 | |
Senior Member
Chris Sideroff
Join Date: Mar 2009
Location: Ottawa, ON, CAN
Posts: 434
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Quote:
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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