Bug#450518: mpicc not found
Package: libopenmpi-dev Version: 1.2.4-3 Severity: grave --- Please enter the report below this line. --- $ wajig install libopenmpi-dev Reading package lists... Done Building dependency tree Reading state information... Done The following packages were automatically installed and are no longer required: libmatheval1 libsuperlu3 libt1-5 libsuperlu3-dev libhdf4g gpsd libwebkitgdk0d xpdf-common Use 'apt-get autoremove' to remove them. The following extra packages will be installed: libopenmpi1 openmpi-common The following NEW packages will be installed: libopenmpi-dev libopenmpi1 openmpi-common 0 upgraded, 3 newly installed, 0 to remove and 2 not upgraded. Need to get 1555kB of archives. After unpacking 6881kB of additional disk space will be used. Do you want to continue [Y/n]? Get:1 http://ftp.cz.debian.org unstable/main libopenmpi1 1.2.4-3 [1059kB] Get:2 http://ftp.cz.debian.org unstable/main openmpi-common 1.2.4-3 [46.4kB] Get:3 http://ftp.cz.debian.org unstable/main libopenmpi-dev 1.2.4-3 [450kB] Fetched 1555kB in 18s (85.3kB/s) Selecting previously deselected package libopenmpi1. (Reading database ... 173852 files and directories currently installed.) Unpacking libopenmpi1 (from .../libopenmpi1_1.2.4-3_i386.deb) ... Selecting previously deselected package openmpi-common. Unpacking openmpi-common (from .../openmpi-common_1.2.4-3_all.deb) ... Selecting previously deselected package libopenmpi-dev. Unpacking libopenmpi-dev (from .../libopenmpi-dev_1.2.4-3_i386.deb) ... Setting up libopenmpi1 (1.2.4-3) ... Setting up openmpi-common (1.2.4-3) ... Setting up libopenmpi-dev (1.2.4-3) ... $ mpicc -bash: mpicc: command not found This temporary fix overcomes the problem: $ sudo ln -s /usr/bin/opal_wrapper /usr/bin/mpicc The same has to be done for all the others: mpif77, mpi90 etc. Ondrej --- System information. --- Architecture: i386 Kernel: Linux 2.6.22-2-686 Debian Release: lenny/sid 500 unstableftp.cz.debian.org --- Package information. --- Depends (Version) | Installed ==-+- libopenmpi1(= 1.2.4-3) | 1.2.4-3 openmpi-common (= 1.2.4-3) | 1.2.4-3 -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#450518: [Pkg-openmpi-maintainers] Bug#450518: mpicc not found
Hello Ondrej! Am Mittwoch, den 07.11.2007, 21:31 +0100 schrieb Ondrej Certik: $ mpicc -bash: mpicc: command not found This temporary fix overcomes the problem: $ sudo ln -s /usr/bin/opal_wrapper /usr/bin/mpicc The same has to be done for all the others: mpif77, mpi90 etc. Thanks for reporting! But I'm unable to reproduce this on amd64 with the same package versions. I have the feeling that somehow the postinst is not executed on your system. Could you please check if - /usr/bin/mpi*.openmpi exist and are pointing to /etc/alternatives? - update-alternatives --display mpicc lists mpicc.openmpi? Thanks! Best regards Manuel -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#450518: [Pkg-openmpi-maintainers] Bug#450518: mpicc not found
Hi Ondrej, Thanks for taking the time to report a bug. On 7 November 2007 at 21:31, Ondrej Certik wrote: | Package: libopenmpi-dev | Version: 1.2.4-3 | Severity: grave | | --- Please enter the report below this line. --- | | $ wajig install libopenmpi-dev At this point, did you have other MPI packages like LAM or MPICH installed? | Reading package lists... Done | Building dependency tree | Reading state information... Done | The following packages were automatically installed and are no longer required: | libmatheval1 libsuperlu3 libt1-5 libsuperlu3-dev libhdf4g gpsd | libwebkitgdk0d xpdf-common | Use 'apt-get autoremove' to remove them. | The following extra packages will be installed: | libopenmpi1 openmpi-common | The following NEW packages will be installed: | libopenmpi-dev libopenmpi1 openmpi-common | 0 upgraded, 3 newly installed, 0 to remove and 2 not upgraded. | Need to get 1555kB of archives. | After unpacking 6881kB of additional disk space will be used. | Do you want to continue [Y/n]? | Get:1 http://ftp.cz.debian.org unstable/main libopenmpi1 1.2.4-3 [1059kB] | Get:2 http://ftp.cz.debian.org unstable/main openmpi-common 1.2.4-3 [46.4kB] | Get:3 http://ftp.cz.debian.org unstable/main libopenmpi-dev 1.2.4-3 [450kB] This *does* install mpicc.openmpi and friends. Did you by chance ever alter the handling of alternatives in /etc/alternatives? | Fetched 1555kB in 18s (85.3kB/s) | Selecting previously deselected package libopenmpi1. | (Reading database ... 173852 files and directories currently installed.) | Unpacking libopenmpi1 (from .../libopenmpi1_1.2.4-3_i386.deb) ... | Selecting previously deselected package openmpi-common. | Unpacking openmpi-common (from .../openmpi-common_1.2.4-3_all.deb) ... | Selecting previously deselected package libopenmpi-dev. | Unpacking libopenmpi-dev (from .../libopenmpi-dev_1.2.4-3_i386.deb) ... | Setting up libopenmpi1 (1.2.4-3) ... | Setting up openmpi-common (1.2.4-3) ... | Setting up libopenmpi-dev (1.2.4-3) ... | | | $ mpicc | -bash: mpicc: command not found | | | This temporary fix overcomes the problem: | | $ sudo ln -s /usr/bin/opal_wrapper /usr/bin/mpicc | | The same has to be done for all the others: mpif77, mpi90 etc. Yes, but it is supposed to be done automatically, and it generally works. I presonally have only experienced problems when I had previously intervened manually (while testing etc). Could you possibly purge the Open MPI packages as well as other MPI packages, and re-start from a clean slate? The packages are generally in decent shape and you should not have this problem. It is worth seeing if we overlooked something. Thanks for your help, Dirk | | | Ondrej | | --- System information. --- | Architecture: i386 | Kernel: Linux 2.6.22-2-686 | | Debian Release: lenny/sid | 500 unstableftp.cz.debian.org | | --- Package information. --- | Depends (Version) | Installed | ==-+- | libopenmpi1(= 1.2.4-3) | 1.2.4-3 | openmpi-common (= 1.2.4-3) | 1.2.4-3 | | | | ___ | Pkg-openmpi-maintainers mailing list | [EMAIL PROTECTED] | http://lists.alioth.debian.org/mailman/listinfo/pkg-openmpi-maintainers -- Three out of two people have difficulties with fractions. -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#450518: [Pkg-openmpi-maintainers] Bug#450518: mpicc not found
Something is wrong with update-alternatives - probably screwed up by mpich, or lam packages. Any ideas? In clean state, this is what I get in pbuilder: # update-alternatives --list mpicc No alternatives for mpicc. # and outside: $ sudo update-alternatives --list mpicc $ Which means this is the problem probably. Ondrej -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#450518: [Pkg-openmpi-maintainers] Bug#450518: mpicc not found
Hi Dirk and Manuel, Thanks for taking the time to report a bug. Thanks for a quick reply. | $ wajig install libopenmpi-dev At this point, did you have other MPI packages like LAM or MPICH installed? Nothing. I purged everything. I installed openmpi. I purged openmpi and checked again everything is purged, installed openmpi. Then did the same procedure on 3 different computers (i386 and amd64). Only then filled a bugreport, after observing the exact same behavior on all of them. Note: I had mpich and lam installed before, but I purged them. This *does* install mpicc.openmpi and friends. Did you by chance ever alter the handling of alternatives in /etc/alternatives? Not manually, but some package has screwed it up, see below. Yes, but it is supposed to be done automatically, and it generally works. I presonally have only experienced problems when I had previously intervened manually (while testing etc). Could you possibly purge the Open MPI packages as well as other MPI packages, and re-start from a clean slate? I did that already before filling this bugreport. The packages are generally in decent shape and you should not have this problem. It is worth seeing if we overlooked something. I tried pbuilder --login and tried the procedure above and it works So something is wrong on all my Debian systems. $ wajig remove libopenmpi1 Reading package lists... Done Building dependency tree Reading state information... Done The following packages will be REMOVED: libopenmpi-dev libopenmpi1 openmpi-bin 0 upgraded, 0 newly installed, 3 to remove and 1 not upgraded. Need to get 0B of archives. After unpacking 7422kB disk space will be freed. Do you want to continue [Y/n]? (Reading database ... 149065 files and directories currently installed.) Removing libopenmpi-dev ... Use of uninitialized value in string eq at /usr/sbin/update-alternatives line 432. Removing openmpi-bin ... Removing libopenmpi1 ... Notice the problem in update-alternatives. I again tried to install libopenmpi-dev and it again doesn't work. I tried installing, removing and installing again in pbuilder - it works. Hm. Something is wrong with update-alternatives - probably screwed up by mpich, or lam packages. Any ideas? Ondrej -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#450518: [Pkg-openmpi-maintainers] Bug#450518: mpicc not found
On Nov 7, 2007 11:24 PM, Ondrej Certik [EMAIL PROTECTED] wrote: Something is wrong with update-alternatives - probably screwed up by mpich, or lam packages. Any ideas? In clean state, this is what I get in pbuilder: # update-alternatives --list mpicc No alternatives for mpicc. # and outside: $ sudo update-alternatives --list mpicc $ Which means this is the problem probably. Ondrej I think I solved the problem. I need to execute: sudo update-alternatives --remove-all mpicc for all the mpi* commands. And it starts working... I wonder how this could happen, I really don't remember touching these by hand. And especially not on all my computers. Ondrej -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#450518: [Pkg-openmpi-maintainers] Bug#450518: mpicc not found
Ondrej, Thanks for your thoroug repplies, and for actually testing all this before you posted :) On 7 November 2007 at 23:26, Ondrej Certik wrote: | I think I solved the problem. I need to execute: | | sudo update-alternatives --remove-all mpicc | | | for all the mpi* commands. And it starts working... I wonder how this | could happen, I really don't remember touching these by hand. And | especially not on all my computers. When I was switching between lam and ompi, something similar happened to me and I also had to resort to update-alternatives. IIRC I used --auto but I didn't write that down. Now, having gotten here, would you agree that is not a bug in the Open MPI packages but rather than some fragility in update-alternatives? Is it ok if we close this? Cheers, Dirk -- Three out of two people have difficulties with fractions. -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#450518: [Pkg-openmpi-maintainers] Bug#450518: mpicc not found
When I was switching between lam and ompi, something similar happened to me and I also had to resort to update-alternatives. IIRC I used --auto but I didn't write that down. Now, having gotten here, would you agree that is not a bug in the Open MPI packages but rather than some fragility in update-alternatives? Is it ok if we close this? Sure, close it. Open MPI seems to be fine. I also managed to build petsc thanks to this. Now I am going to try to fix libmesh and petsc4py. Ondrej -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#450518: [Pkg-openmpi-maintainers] Bug#450518: Bug#450518: mpicc not found
Am Mittwoch, den 07.11.2007, 23:58 +0100 schrieb Ondrej Certik: Sure, close it. Open MPI seems to be fine. Thanks! We put a lot of effort in it and are very happy it's appreciated! :) I'll close the bug then. I also managed to build petsc thanks to this. Now I am going to try to fix libmesh and petsc4py. Happy Hacking! Best regards Manuel -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
