CFD Online Logo CFD Online URL
www.cfd-online.com
[Sponsors]
Home > Forums > Software User Forums > OpenFOAM > OpenFOAM Installation

[foam-extend.org] Error compiling OpenFOAM-1.6-ext

Register Blogs Members List Search Today's Posts Mark Forums Read

Like Tree6Likes

Reply
 
LinkBack Thread Tools Search this Thread Display Modes
Old   December 24, 2010, 06:18
Default
  #61
Member
 
Giovanni Caramia
Join Date: Mar 2009
Location: Bari, ITALY
Posts: 58
Rep Power: 17
karamiag is on a distinguished road
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
========================================
karamiag is offline   Reply With Quote

Old   January 6, 2011, 15:50
Default
  #62
Senior Member
 
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
Rep Power: 17
boger is on a distinguished road
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
__________________
David A. Boger
boger is offline   Reply With Quote

Old   January 6, 2011, 18:35
Default
  #63
Senior Member
 
Martin Beaudoin
Join Date: Mar 2009
Posts: 332
Rep Power: 22
mbeaudoin will become famous soon enough
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
mbeaudoin is offline   Reply With Quote

Old   January 6, 2011, 22:46
Default
  #64
Senior Member
 
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
Rep Power: 17
boger is on a distinguished road
Martin- Thanks. That sounds great. I'll work on putting something together.
__________________
David A. Boger
boger is offline   Reply With Quote

Old   January 15, 2011, 18:07
Default
  #65
Member
 
Mathieu Olivier
Join Date: Mar 2009
Location: Quebec City, Canada
Posts: 77
Rep Power: 17
mathieu is on a distinguished road
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
mathieu is offline   Reply With Quote

Old   January 15, 2011, 18:10
Default
  #66
Senior Member
 
lakeat's Avatar
 
Daniel WEI (老魏)
Join Date: Mar 2009
Location: Beijing, China
Posts: 689
Blog Entries: 9
Rep Power: 21
lakeat is on a distinguished road
Send a message via Skype™ to lakeat
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.
__________________
~
Daniel WEI
-------------
Boeing Research & Technology - China
Beijing, China
Email
lakeat is offline   Reply With Quote

Old   January 15, 2011, 18:25
Default
  #67
Member
 
Mathieu Olivier
Join Date: Mar 2009
Location: Quebec City, Canada
Posts: 77
Rep Power: 17
mathieu is on a distinguished road
Dear Daniel,

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

export WM_MPLIB=SYSTEMOPENMPI

Mathieu
mathieu is offline   Reply With Quote

Old   January 15, 2011, 18:33
Default
  #68
Senior Member
 
lakeat's Avatar
 
Daniel WEI (老魏)
Join Date: Mar 2009
Location: Beijing, China
Posts: 689
Blog Entries: 9
Rep Power: 21
lakeat is on a distinguished road
Send a message via Skype™ to lakeat
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`
__________________
~
Daniel WEI
-------------
Boeing Research & Technology - China
Beijing, China
Email
lakeat is offline   Reply With Quote

Old   January 15, 2011, 18:48
Default
  #69
Member
 
Mathieu Olivier
Join Date: Mar 2009
Location: Quebec City, Canada
Posts: 77
Rep Power: 17
mathieu is on a distinguished road
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...
zcjwyl likes this.
mathieu is offline   Reply With Quote

Old   January 15, 2011, 18:56
Default
  #70
Senior Member
 
lakeat's Avatar
 
Daniel WEI (老魏)
Join Date: Mar 2009
Location: Beijing, China
Posts: 689
Blog Entries: 9
Rep Power: 21
lakeat is on a distinguished road
Send a message via Skype™ to lakeat
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,
__________________
~
Daniel WEI
-------------
Boeing Research & Technology - China
Beijing, China
Email
lakeat is offline   Reply With Quote

Old   January 16, 2011, 19:02
Default
  #71
Member
 
Mathieu Olivier
Join Date: Mar 2009
Location: Quebec City, Canada
Posts: 77
Rep Power: 17
mathieu is on a distinguished road
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
zcjwyl likes this.
mathieu is offline   Reply With Quote

Old   January 21, 2011, 17:24
Default
  #72
Senior Member
 
Chris Sideroff
Join Date: Mar 2009
Location: Ottawa, ON, CAN
Posts: 434
Rep Power: 22
cnsidero is on a distinguished road
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.
cnsidero is offline   Reply With Quote

Old   January 22, 2011, 07:01
Default
  #73
Member
 
Giovanni Caramia
Join Date: Mar 2009
Location: Bari, ITALY
Posts: 58
Rep Power: 17
karamiag is on a distinguished road
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.
karamiag is offline   Reply With Quote

Old   January 28, 2011, 09:56
Default
  #74
Senior Member
 
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
Rep Power: 17
boger is on a distinguished road
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
__________________
David A. Boger
boger is offline   Reply With Quote

Old   January 28, 2011, 10:13
Default
  #75
Senior Member
 
Laurence R. McGlashan
Join Date: Mar 2009
Posts: 370
Rep Power: 23
l_r_mcglashan will become famous soon enough
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.
__________________
Laurence R. McGlashan :: Website
l_r_mcglashan is offline   Reply With Quote

Old   January 28, 2011, 11:16
Default
  #76
Senior Member
 
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
Rep Power: 17
boger is on a distinguished road
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.
__________________
David A. Boger
boger is offline   Reply With Quote

Old   January 28, 2011, 11:25
Default
  #77
Senior Member
 
Laurence R. McGlashan
Join Date: Mar 2009
Posts: 370
Rep Power: 23
l_r_mcglashan will become famous soon enough
I see. Does this help? Otherwise I'm stuck.

https://www.redhat.com/archives/rpm-.../msg00048.html
__________________
Laurence R. McGlashan :: Website
l_r_mcglashan is offline   Reply With Quote

Old   January 28, 2011, 11:40
Default
  #78
Senior Member
 
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
Rep Power: 17
boger is on a distinguished road
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
__________________
David A. Boger
boger is offline   Reply With Quote

Old   January 28, 2011, 12:50
Default
  #79
Senior Member
 
David Boger
Join Date: Mar 2009
Location: Penn State Applied Research Laboratory
Posts: 146
Rep Power: 17
boger is on a distinguished road
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!
__________________
David A. Boger
boger is offline   Reply With Quote

Old   February 2, 2011, 20:37
Default
  #80
Senior Member
 
Chris Sideroff
Join Date: Mar 2009
Location: Ottawa, ON, CAN
Posts: 434
Rep Power: 22
cnsidero is on a distinguished road
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?
cnsidero is offline   Reply With Quote

Reply

Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are Off
Pingbacks are On
Refbacks are On


Similar Threads
Thread Thread Starter Forum Replies Last Post
Frequently Asked Questions about Installing OpenFOAM wyldckat OpenFOAM Installation 3 November 14, 2023 12:58
OpenFOAM Training, London, Chicago, Munich, Houston 2016-2017 cfd.direct OpenFOAM Announcements from Other Sources 0 September 14, 2016 04:19
New OpenFOAM Forum Structure jola OpenFOAM 2 October 19, 2011 07:55
OpenFOAM 1.6 package - CentOS 5.3 x86_64 linnemann OpenFOAM Installation 36 September 2, 2009 13:46
OpenFOAM Version 1.6 Released opencfd OpenFOAM Announcements from ESI-OpenCFD 0 July 27, 2009 18:55


All times are GMT -4. The time now is 21:26.