Re: [OMPI users] unable to open osc pt2pt
I don't know how to access the svn repository. svn checkout http://mpi4py.scipy.org/mpi4py/browser/mpi4py/trunk mpi4py svn: PROPFIND request failed on '/mpi4py/browser/mpi4py/trunk' svn: PROPFIND of '/mpi4py/browser/mpi4py/trunk': 200 Ok (http://mpi4py.scipy.org) Also signed up for the mpi4py users list; took many days to get a reply and when I confirmed the subscription e-mail, it bounced back; maybe a temporary problem?... Thanks for any help. -- Valmor > -Original Message- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > Behalf Of Brian Granger > Sent: Monday, December 17, 2007 10:47 AM > To: Open MPI Users > Subject: Re: [OMPI users] unable to open osc pt2pt > > This should be fixed in the subversion trunk of mpi4py. Can you do an > update to that version and retry. If it still doesn't work, post to > the mpi4py list and we will see what we can do. > > Brian > > On Dec 17, 2007 8:25 AM, de Almeida, Valmor F. <dealmei...@ornl.gov> > wrote: > > > > Hello, > > > > I am getting these messages (below) when running mpi4py python codes. > > Always one message per mpi process. The codes seem to run correctly. Any > > ideas why this is happening and how to avoid it? > > > > Thanks, > > > > -- > > Valmor de Almeida > > > > >mpirun -np 2 python helloworld.py > > [xeon0:05998] mca: base: component_find: unable to open osc pt2pt: file > > not found (ignored) > > [xeon0:05999] mca: base: component_find: unable to open osc pt2pt: file > > not found (ignored) > > Hello, World!! I am process 0 of 2 on xeon0. > > Hello, World!! I am process 1 of 2 on xeon0. > > > > > > > > ___ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
[OMPI users] unable to open osc pt2pt
Hello, I am getting these messages (below) when running mpi4py python codes. Always one message per mpi process. The codes seem to run correctly. Any ideas why this is happening and how to avoid it? Thanks, -- Valmor de Almeida >mpirun -np 2 python helloworld.py [xeon0:05998] mca: base: component_find: unable to open osc pt2pt: file not found (ignored) [xeon0:05999] mca: base: component_find: unable to open osc pt2pt: file not found (ignored) Hello, World!! I am process 0 of 2 on xeon0. Hello, World!! I am process 1 of 2 on xeon0.
Re: [OMPI users] Configure fails with icc 10.1.008
Eric,
I see you are using a gentoo distro like me. My version uses the vanilla
kernel 2.6.22.9 and gcc-4.1.2. I have the following intel compiler
versions installed:
10.0.026 10.1.008 10.1.011 9.1.052
None of them are able to build a functional version of openmpi-1.2.4.
I've been posting this problem to this list and also to the Intel
premier customer support. The actual problem is that after building
openmpi, I get:
->ompi_info
Segmentation fault
->mpic++ --showme
Segmentation fault
The compilers do work outside openmpi. I can compile and run non-mpi
programs.
Please post to this list whether you are able to compile and get a
working openmpi with gcc-4.1 series.
Thanks,
--
Valmor
> -Original Message-
> From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org]
On
> Behalf Of Eric Thibodeau
> Sent: Friday, December 07, 2007 11:14 AM
> To: Jeff Squyres
> Cc: Open MPI Users
> Subject: Re: [OMPI users] Configure fails with icc 10.1.008
>
> Jeff,
>
> Thanks...at 23h30 coffee is far off... I saw the proper section of
> the config.log showing exactly that (hello world not working). For
> everyone else's benefit, ICC (up to 10.1.008) is _not_ compatible with
> GCC 4.2... (guess I'll have to retro back to 4.1 series...)
>
> Eric
>
> Jeff Squyres wrote:
> > This is not an Open MPI problem; Open MPI is simply reporting that
> > your C++ compiler is not working. OMPI tests a trivial C++ program
> > that uses the STL to ensure that your C++ program is working. It's
> > essentially:
> >
> > #include
> > int
> > main ()
> > {
> > std::string foo = "Hello, world"
> > ;
> > return 0;
> > }
> >
> > You should probably check with Intel support for more details.
> >
> >
> >
> > On Dec 6, 2007, at 11:25 PM, Eric Thibodeau wrote:
> >
> >> Hello all,
> >>
> >> I am unable to get past ./configure as ICC fails on C++ tests
(see
> >> attached ompi-output.tar.gz). Configure was called without and the
> >> with sourcing `/opt/intel/cc/10.1.xxx/bin/iccvars.sh` as per one
of
> >> the invocation options in icc's doc. I was unable to find the
> >> relevant (well..intelligible for me that is ;P ) cause of the
failure
> >> in config.log. Any help would be appreciated.
> >>
> >> Thanks,
> >>
> >> Eric Thibodeau
> >> ___
> >> users mailing list
> >> us...@open-mpi.org
> >> http://www.open-mpi.org/mailman/listinfo.cgi/users
> >
> >
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] suggested intel compiler version for openmpi-1.2.4
> -Original Message- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > Behalf Of Jeff Squyres > > If Intel is telling you that they don't support your glibc version, I > wouldn't be surprised by random segv's in any application that you > build on that platform (including Open MPI). The install script of the 10.1.008 suite lists the supported platform. That includes kernel 2.6 and glibc 2.6. I guess there are some loose ends. -- Valmor > > > > On Dec 5, 2007, at 9:59 AM, de Almeida, Valmor F. wrote: > > > > > > > Attached is the config.log file for intel 9.1.052. I've also tried the > > intel 10.1.008 and posted to this list the config.log on a previous > > e-mail (12/2/2007). > > > > Here are the key commands for building and installing > > > > export FC=ifort > > export F77=ifort > > export CXX=icpc > > export CC=icc > > > > ./configure --prefix=/usr/local/packages/openmpi-1.2.4_intel-9.1.052 > > --with-mpi-param_check=always --with-mpi-f90-size=medium > > --with-f90-max-array-dim=4 CC=icc CXX=icpc F90=ifort F77=ifort > > > > make -j 2 > > make -j 2 install > > > > Here is some info on my system > > > > ->emerge --info > > Portage 2.1.3.19 (default-linux/x86/2007.0, gcc-4.1.2, glibc-2.6.1-r0, > > 2.6.22.9 i686) > > = > > System uname: 2.6.22.9 i686 Intel(R) Xeon(TM) CPU 2.66GHz > > Timestamp of tree: Sat, 17 Nov 2007 04:30:01 + > > app-shells/bash: 3.2_p17 > > dev-java/java-config: 1.3.7, 2.0.33-r1 > > dev-lang/python: 2.4.4-r6 > > dev-python/pycrypto: 2.0.1-r6 > > sys-apps/baselayout: 1.12.9-r2 > > sys-apps/sandbox:1.2.18.1-r2 > > sys-devel/autoconf: 2.13, 2.61-r1 > > sys-devel/automake: 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 > > sys-devel/binutils: 2.18-r1 > > sys-devel/gcc-config: 1.3.16 > > sys-devel/libtool: 1.5.24 > > virtual/os-headers: 2.6.22-r2 > > > > Here is > > > > ->echo $PATH > > /opt/cubit:/opt/gambit/bin:/opt/compilers/intel/idb/9.1.052/bin:/opt/ > > com > > pilers/intel/fc/9.1.052/bin:/opt/compilers/intel/cc/9.1.052/bin:/usr/ > > loc > > al/nwchem/bin:/usr/local/visit/bin:/usr/local/ompi_intel/bin:/usr/ > > local/ > > sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/i686- > > pc- > > linux-gnu/gcc-bin/4.1.2:/usr/local/packages/cca- > > tools-0.6.4_gcc-4.1.2/bi > > n:/usr/bin:/opt/chpl/bin/linux > > > > Here is > > > > ->echo $LD_LIBRARY_PATH > > /opt/compilers/intel/fc/9.1.052/lib:/opt/compilers/intel/cc/9.1.052/ > > lib: > > /usr/local/ompi_intel/lib::/usr/local/packages/cca- > > tools-0.6.4_gcc-4.1.2 > > /lib > > > > > > I am also copying this to the person at Intel who is looking at the > > problem, and here is a posting from the Intel Premier Support (Issue > > number: 461117) for this case > > > > > > 12/04/2007 > > Valmor, > > Thanks for your submission. The Intel compilers have supported the 2.6 > > Linux kernel for some time now, but they do not yet support glibc 2.6. > > The most recent version of glibc supported is 2.5, as represented by > > the > > Red Hat Enterprise Linux 5 and Ubuntu 7.04 distributions. There are > > known issues with Ubuntu 7.10, for example, which has a later glibc. > > What version of Gentoo are you using, and do you have the option to > > try > > an older glibc and gcc along with the Intel compiler version 10.1? > > > > It's not sure that the glibc version is the problem, so I will try to > > build OpenMPI with glibc 2.5 on Red Hat EL5 or Ubuntu 7.04 to see if > > that shows any problems. > > > > Regards, > > Martyn > > > > 12/05/2007 > > Martyn, > > > > During the installation of 10.1.008, the install script says that > > glibc > > 2.6 is supported. > > > > -- > > Valmor > > > > > > Thanks for your help. > > > > -- > > Valmor > > > > > > > > > > > > > > > > > >> -Original Message- > >> From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] > > On > >> Behalf Of Jeff Squyres > >> Sent: Tuesday, December 04, 2007 5:58 PM > >> To: Open MPI Users > >> Subject: Re: [OMPI users] suggested intel compiler version for > > openmpi- > >> 1.2.4 > >> > >> I have compiled Open MPI with Int
Re: [OMPI users] suggested intel compiler version for openmpi-1.2.4
Attached is the config.log file for intel 9.1.052. I've also tried the intel 10.1.008 and posted to this list the config.log on a previous e-mail (12/2/2007). Here are the key commands for building and installing export FC=ifort export F77=ifort export CXX=icpc export CC=icc ./configure --prefix=/usr/local/packages/openmpi-1.2.4_intel-9.1.052 --with-mpi-param_check=always --with-mpi-f90-size=medium --with-f90-max-array-dim=4 CC=icc CXX=icpc F90=ifort F77=ifort make -j 2 make -j 2 install Here is some info on my system ->emerge --info Portage 2.1.3.19 (default-linux/x86/2007.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.22.9 i686) = System uname: 2.6.22.9 i686 Intel(R) Xeon(TM) CPU 2.66GHz Timestamp of tree: Sat, 17 Nov 2007 04:30:01 + app-shells/bash: 3.2_p17 dev-java/java-config: 1.3.7, 2.0.33-r1 dev-lang/python: 2.4.4-r6 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.9-r2 sys-apps/sandbox:1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.3.16 sys-devel/libtool: 1.5.24 virtual/os-headers: 2.6.22-r2 Here is ->echo $PATH /opt/cubit:/opt/gambit/bin:/opt/compilers/intel/idb/9.1.052/bin:/opt/com pilers/intel/fc/9.1.052/bin:/opt/compilers/intel/cc/9.1.052/bin:/usr/loc al/nwchem/bin:/usr/local/visit/bin:/usr/local/ompi_intel/bin:/usr/local/ sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/i686-pc- linux-gnu/gcc-bin/4.1.2:/usr/local/packages/cca-tools-0.6.4_gcc-4.1.2/bi n:/usr/bin:/opt/chpl/bin/linux Here is ->echo $LD_LIBRARY_PATH /opt/compilers/intel/fc/9.1.052/lib:/opt/compilers/intel/cc/9.1.052/lib: /usr/local/ompi_intel/lib::/usr/local/packages/cca-tools-0.6.4_gcc-4.1.2 /lib I am also copying this to the person at Intel who is looking at the problem, and here is a posting from the Intel Premier Support (Issue number: 461117) for this case 12/04/2007 Valmor, Thanks for your submission. The Intel compilers have supported the 2.6 Linux kernel for some time now, but they do not yet support glibc 2.6. The most recent version of glibc supported is 2.5, as represented by the Red Hat Enterprise Linux 5 and Ubuntu 7.04 distributions. There are known issues with Ubuntu 7.10, for example, which has a later glibc. What version of Gentoo are you using, and do you have the option to try an older glibc and gcc along with the Intel compiler version 10.1? It's not sure that the glibc version is the problem, so I will try to build OpenMPI with glibc 2.5 on Red Hat EL5 or Ubuntu 7.04 to see if that shows any problems. Regards, Martyn 12/05/2007 Martyn, During the installation of 10.1.008, the install script says that glibc 2.6 is supported. -- Valmor Thanks for your help. -- Valmor > -Original Message- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > Behalf Of Jeff Squyres > Sent: Tuesday, December 04, 2007 5:58 PM > To: Open MPI Users > Subject: Re: [OMPI users] suggested intel compiler version for openmpi- > 1.2.4 > > I have compiled Open MPI with Intel 10.0 and 9.1 with no problems on > RHEL4U4. > > Can you send all the info that you can (obviously, ompi_info won't > run) from http://www.open-mpi.org/community/help/ ? > > > > On Dec 4, 2007, at 4:26 PM, de Almeida, Valmor F. wrote: > > > > > Hello, > > > > What is the suggested intel compiler version to compile openmpi-1.2.4? > > > > I tried versions 10.1.008 and 9.1.052 and no luck in getting a working > > library. In both cases I get: > > > > ->mpic++ --showme > > Segmentation fault > > > > ->ompi_info > > Segmentation fault > > > > Thanks for your help. > > > > -- > > Valmor de Almeida > > > > > > > > > > > > ___ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > -- > Jeff Squyres > Cisco Systems > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users config.log.bz2 Description: config.log.bz2
[OMPI users] suggested intel compiler version for openmpi-1.2.4
Hello, What is the suggested intel compiler version to compile openmpi-1.2.4? I tried versions 10.1.008 and 9.1.052 and no luck in getting a working library. In both cases I get: ->mpic++ --showme Segmentation fault ->ompi_info Segmentation fault Thanks for your help. -- Valmor de Almeida
Re: [OMPI users] Segmentation fault: intel 10.1.008 compilers w/openmpi-1.2.4
> -Original Message- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > > On Tue, 2007-12-04 at 09:33 +0100, Åke Sandgren wrote: > > On Sun, 2007-12-02 at 21:27 -0500, de Almeida, Valmor F. wrote: > > > > Run an nm on opal/mca/memory/ptmalloc2/.libs/malloc.o and check if > > malloc is defined in there. > > > > This seems to be the problem i have when compiling with pathscale. > > It removes the malloc (public_mALLOc) function from the objectfile but > > leaves the free (public_fREe) in there, resulting in malloc/free > > mismatch. > > For pathscale the solution for me was to add -fno-builtin. > Now ompi_info doesn't segfault anymore. > > Check if the intel 10 has something similar. Below is the nm output. The no builtin compiler option you mentioned above seems to belong to gcc. I have compiled openmpi-1.2.4 with the gcc-4.1.2 suite without problems. Thanks, -- Valmor ->nm ./opal/mca/memory/ptmalloc2/.libs/malloc.o | grep -i "malloc" 3faa T __malloc_check_init 0004 D __malloc_hook 08b8 B __malloc_initialize_hook 0010 D __malloc_initialized 3944 t _int_icomalloc 0c36 T _int_malloc 08b0 b disallow_malloc_check 3742 T independent_comalloc 06a8 T malloc t malloc_atfork 2224 t malloc_check 1184 t malloc_consolidate 2c00 T malloc_get_state 0410 t malloc_hook_ini 44f2 t malloc_init_state 2d84 T malloc_set_state 2b5e t malloc_starter 3ad4 T malloc_trim 3b5e T malloc_usable_size U opal_mem_free_ptmalloc2_mmap U opal_mem_free_ptmalloc2_munmap 17d6 t opal_mem_free_ptmalloc2_sbrk 4032 t ptmalloc_init 44b0 t ptmalloc_init_minimal 01dc t ptmalloc_lock_all 02f6 t ptmalloc_unlock_all 036a t ptmalloc_unlock_all2 129e t sYSMALLOc 0870 b save_malloc_hook 08ac b using_malloc_checking
[OMPI users] Segmentation fault: intel 10.1.008 compilers w/ openmpi-1.2.4
Hello, After compiling ompi-1.2.4 with the intel compiler suite 10.1.008, I get ->mpicxx --showme Segmentation fault ->ompi_info Segmentation fault The 10.1.008 is the only one I know that officially supports the linux kernel 2.6 and glibc-2.6 that I have on my system. config.log file attached. Any help appreciated. Thanks, -- Valmor de Almeida config.log.bz2 Description: config.log.bz2
Re: [OMPI users] warning:regcache incompatible with malloc
Thanks, -- Valmor > -Original Message- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > Behalf Of Tim Prins > Sent: Tuesday, November 27, 2007 10:37 AM > To: Open MPI Users > Subject: Re: [OMPI users] warning:regcache incompatible with malloc > > Hi Valmor, > > I prefer to just set the environment variable in my .bashrc so I never > have to think about it again. Also it might be slightly better since > Open MPI tries to be network neutral, and linking the application > against the Myrinet libraries violates that principle. But if you are > only ever going to use the particular compilation with Myrinet anyways, > I suppose it does not matter. > > I guess this is a long way of saying that it is just personal preference. > > Hope this helps, > > Tim > > > de Almeida, Valmor F. wrote: > > Hello, > > > > I am getting the warnings after an upgrade to > > mx-1.2.4 and openmpi-1.2.4. > > > > Either using the env variable setting MX_RCACHE=2, or linking the > > application with -lmyriexpress removes the warnings. > > > > Is either one of them the preferred way of doing it? > > > > Thanks, > > > > -- > > Valmor > > > >> -Original Message- > >> From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] > > On > >> Behalf Of Scott Atchley > >> Sent: Tuesday, July 10, 2007 3:31 PM > >> To: Open MPI Users > >> Subject: Re: [OMPI users] warning:regcache incompatible with malloc > >> > >> On Jul 10, 2007, at 3:24 PM, Tim Prins wrote: > >> > >>> On Tuesday 10 July 2007 03:11:45 pm Scott Atchley wrote: > >>>> On Jul 10, 2007, at 2:58 PM, Scott Atchley wrote: > >>>>> Tim, starting with the recently released 1.2.1, it is the default. > >>>> To clarify, MX_RCACHE=1 is the default. > >>> It would be good for the default to be something where there is no > >>> warning > >>> printed (i.e. 0 or 2). I see the warning on the current trunk. > >>> > >>> Tim > >> After further discussion in-house, the warning can be avoided if - > >> lmyriexpress is included when linking the app (i.e. if it is in mpicc > >> when linking). > >> > >> Another clarification, the regache does work with several replacement > >> malloc libraries. If the user application overloads mmap(), munmap() > >> and sbrk(), then it may or may not work. In this case, the user > >> should use MX_RCACHE=0. > >> > >> Scott > >> ___ > >> users mailing list > >> us...@open-mpi.org > >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > ___ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] warning:regcache incompatible with malloc
Hello, I am getting the warnings after an upgrade to mx-1.2.4 and openmpi-1.2.4. Either using the env variable setting MX_RCACHE=2, or linking the application with -lmyriexpress removes the warnings. Is either one of them the preferred way of doing it? Thanks, -- Valmor > -Original Message- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > Behalf Of Scott Atchley > Sent: Tuesday, July 10, 2007 3:31 PM > To: Open MPI Users > Subject: Re: [OMPI users] warning:regcache incompatible with malloc > > On Jul 10, 2007, at 3:24 PM, Tim Prins wrote: > > > On Tuesday 10 July 2007 03:11:45 pm Scott Atchley wrote: > >> On Jul 10, 2007, at 2:58 PM, Scott Atchley wrote: > >>> Tim, starting with the recently released 1.2.1, it is the default. > >> > >> To clarify, MX_RCACHE=1 is the default. > > > > It would be good for the default to be something where there is no > > warning > > printed (i.e. 0 or 2). I see the warning on the current trunk. > > > > Tim > > After further discussion in-house, the warning can be avoided if - > lmyriexpress is included when linking the app (i.e. if it is in mpicc > when linking). > > Another clarification, the regache does work with several replacement > malloc libraries. If the user application overloads mmap(), munmap() > and sbrk(), then it may or may not work. In this case, the user > should use MX_RCACHE=0. > > Scott > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
[OMPI users] mpi python recommendation
Hello list, I would appreciate recommendations on what to use for developing mpi python codes. I've seen several packages on public domain: mympi, pypar, mpi python, mpi4py and it would be helpful to start in the right direction. Thanks, -- Valmor de Almeida ORNL PS. I apologize if this message appears twice in the list but something weird happened with my first send; probably a local problem on my side.
Re: [OMPI users] OpenMPI 1.2 on MacOSX Intel Fails
> -Original Message- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > Behalf Of Brian Powell > > using gcc and ifort (see the attached config.log) with a variety of One recommendation I received from this list was not to mix compiler suites. So use icpc/icc/ifort or gcc/g++/gfortran. I need to use the former combination since gfortran does not compile some necessary legacy fortran codes. -- Valmor
[OMPI users] mca_btl_tcp_frag_send: writev failed with errno=104
Hello, Is there a way to get detailed information on what this error may be? [x1:17287] mca_btl_tcp_frag_send: writev failed with errno=104 mpirun noticed that job rank 0 with PID 17287 on node x1 exited on signal 15 (Terminated). 15 additional processes aborted (not shown) Thanks, -- Valmor Using MX-1.1.6 and ->ompi_info Open MPI: 1.2.1a0r14250 Open MPI SVN revision: r14250 Open RTE: 1.2.1a0r14250 Open RTE SVN revision: r14250 OPAL: 1.2.1a0r14250 OPAL SVN revision: r14250 Prefix: /opt/intel-openmpi-1.2.1a0r14250 Configured architecture: i686-pc-linux-gnu Configured by: root C bindings: yes C++ bindings: yes Fortran77 bindings: yes (all) Fortran90 bindings: yes Fortran90 bindings size: medium C compiler: icc C compiler absolute: /opt/icc-9.1.047/bin/icc C++ compiler: icpc C++ compiler absolute: /opt/icc-9.1.047/bin/icpc Fortran77 compiler: ifort Fortran77 compiler abs: /opt/ifort-9.1.041/bin/ifort Fortran90 compiler: ifort Fortran90 compiler abs: /opt/ifort-9.1.041/bin/ifort C profiling: yes C++ profiling: yes Fortran77 profiling: yes Fortran90 profiling: yes C++ exceptions: no Thread support: posix (mpi: no, progress: no) Internal debug support: no MPI parameter check: always Memory profiling support: no Memory debugging support: no libltdl support: yes Heterogeneous support: yes mpirun default --prefix: no MCA backtrace: execinfo (MCA v1.0, API v1.0, Component v1.2.1) MCA memory: ptmalloc2 (MCA v1.0, API v1.0, Component v1.2.1) MCA paffinity: linux (MCA v1.0, API v1.0, Component v1.2.1) MCA maffinity: first_use (MCA v1.0, API v1.0, Component v1.2.1) MCA timer: linux (MCA v1.0, API v1.0, Component v1.2.1) MCA allocator: basic (MCA v1.0, API v1.0, Component v1.0)
Re: [OMPI users] experiences with gfortran and ompi
> -Original Message- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > Behalf Of Jeff Squyres > > Bummer. FWIW, we have some internal testing OMPI Fortran codes that > are difficult to get to compile uniformly across all Fortran > compilers (the most difficult point is usually fortran pointers). Same experience here with fortran pointers. > As Rainer said, we don't recommend this. It may be possible, but I Thanks for the inputs. I am creating two builds of ompi for the suites: gcc/g++/gfortran (4.1.1) and icc/icc/ifort (9.1). -- Valmor
Re: [OMPI users] mca_btl_mx_init: mx_open_endpoint() failed withstatus=20
Hi Tim, I installed the openmpi-1.2.1a0r14178 tarball (took this opportunity to use the intel fortran compiler instead gfortran). With a simple test it seems to work but note the same messages ->mpirun -np 8 -machinefile mymachines a.out [x1:25417] mca_btl_mx_init: mx_open_endpoint() failed with status=20 [x1:25418] mca_btl_mx_init: mx_open_endpoint() failed with status=20 [x2:31983] mca_btl_mx_init: mx_open_endpoint() failed with status=20 [x2:31982] mca_btl_mx_init: mx_open_endpoint() failed with status=20 [x2:31980] mca_btl_mx_init: mx_open_endpoint() failed with status=20 Hello, world! I am 4 of 7 Hello, world! I am 0 of 7 Hello, world! I am 1 of 7 Hello, world! I am 5 of 7 Hello, world! I am 2 of 7 Hello, world! I am 7 of 7 Hello, world! I am 6 of 7 Hello, world! I am 3 of 7 and the machinefile is x1 slots=4 max_slots=4 x2 slots=4 max_slots=4 However with a realistic code, it starts fine (same messages as above) and somewhere later: [x1:25947] *** Process received signal *** [x1:25947] Signal: Segmentation fault (11) [x1:25947] Signal code: Address not mapped (1) [x1:25947] Failing at address: 0x14 [x1:25947] [ 0] [0xb7f00440] [x1:25947] [ 1] /opt/openmpi-1.2.1a0r14178/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_r equest_start_copy+0x13e) [0xb7a80e6e] [x1:25947] [ 2] /opt/openmpi-1.2.1a0r14178/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_r equest_process_pending+0x1e3) [0xb7a82463] [x1:25947] [ 3] /opt/openmpi-1.2.1a0r14178/lib/openmpi/mca_pml_ob1.so [0xb7a7ebf8] [x1:25947] [ 4] /opt/openmpi-1.2.1a0r14178/lib/openmpi/mca_btl_sm.so(mca_btl_sm_componen t_progress+0x1813) [0xb7a41923] [x1:25947] [ 5] /opt/openmpi-1.2.1a0r14178/lib/openmpi/mca_bml_r2.so(mca_bml_r2_progress +0x36) [0xb7a4fdd6] [x1:25947] [ 6] /opt/ompi/lib/libopen-pal.so.0(opal_progress+0x79) [0xb7dc41a9] [x1:25947] [ 7] /opt/ompi/lib/libmpi.so.0(ompi_request_wait_all+0xb5) [0xb7e90145] [x1:25947] [ 8] /opt/openmpi-1.2.1a0r14178/lib/openmpi/mca_coll_tuned.so(ompi_coll_tuned _sendrecv_actual+0xc9) [0xb7a167a9] [x1:25947] [ 9] /opt/openmpi-1.2.1a0r14178/lib/openmpi/mca_coll_tuned.so(ompi_coll_tuned _barrier_intra_recursivedoubling+0xe4) [0xb7a1bfb4] [x1:25947] [10] /opt/openmpi-1.2.1a0r14178/lib/openmpi/mca_coll_tuned.so(ompi_coll_tuned _barrier_intra_dec_fixed+0x48) [0xb7a16a18] [x1:25947] [11] /opt/ompi/lib/libmpi.so.0(PMPI_Barrier+0x69) [0xb7ea4059] [x1:25947] [12] driver0(_ZNK3MPI4Comm7BarrierEv+0x20) [0x806baf4] [x1:25947] [13] driver0(_ZN3gms12PartitionSet14ReadData_Case2Ev+0xc92) [0x808bb78] [x1:25947] [14] driver0(_ZN3gms12PartitionSet8ReadDataESsSsSst+0xbc) [0x8086f96] [x1:25947] [15] driver0(main+0x181) [0x8068c7f] [x1:25947] [16] /lib/libc.so.6(__libc_start_main+0xdc) [0xb7b6a824] [x1:25947] [17] driver0(__gxx_personality_v0+0xb9) [0x8068991] [x1:25947] *** End of error message *** mpirun noticed that job rank 0 with PID 25945 on node x1 exited on signal 15 (Terminated). 7 additional processes aborted (not shown) This code does run to completion using ompi-1.2 if I use only 2 slots per machine. Thanks for any help. -- Valmor > -Original Message- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > Behalf Of Tim Prins > Sent: Friday, March 30, 2007 10:49 PM > To: Open MPI Users > Subject: Re: [OMPI users] mca_btl_mx_init: mx_open_endpoint() failed > withstatus=20 > > Hi Valmor, > > What is happening here is that when Open MPI tries to create MX endpoint > for > communication, mx returns code 20, which is MX_BUSY. > > At this point we should gracefully move on, but there is a bug in Open MPI > 1.2 > which causes a segmentation fault in case of this type of error. This will > be > fixed in 1.2.1, and the fix is available now in the 1.2 nightly tarballs. > > Hope this helps, > > Tim > > On Friday 30 March 2007 05:06 pm, de Almeida, Valmor F. wrote: > > Hello, > > > > I am getting this error any time the number of processes requested per > > machine is greater than the number of cpus. I suspect it is something on > > the configuration of mx / ompi that I am missing since another machine I > > have without mx installed runs ompi correctly with oversubscription. > > > > Thanks for any help. > > > > -- > > Valmor > > > > > > ->mpirun -np 3 --machinefile mymachines-1 a.out > > [x1:23624] mca_btl_mx_init: mx_open_endpoint() failed with status=20 > > [x1:23624] *** Process received signal *** [x1:23624] Signal: > > Segmentation fault (11) [x1:23624] Signal code: Address not mapped (1) > > [x1:23624] Failing at address: 0x20 [x1:23624] [ 0] [0xb7f7f440] > > [x1:23624] [ 1] > > /opt/openmpi-1.2/lib/openmpi/mca_btl_mx.so(mca_btl_mx_finalize+0x25) > > [0xb7aca825] [x1:23624] [ 2] > > /opt/openmpi-1.2/lib/openmpi/mca_btl_mx.so(mca_btl_mx_component_init+0x6 > > f8) [0xb7acc658
[OMPI users] experiences with gfortran and ompi
Hello, I would be interested in hearing folk's experiences with gfortran and ompi-1.2. Is gfortran good enough for prime time? I have built ompi-1.2 with gfortran-4.1.1 but no luck in testing it because my application of interest (legacy fortran code) will not compile with gfortran. In addition I would be interested in hearing about the use of different fortran compilers. For instance, how about building ompi with gfortran but compiling mpi fortran codes with the intel compiler? Thanks, -- Valmor
Re: [OMPI users] mca_btl_mx_init: mx_open_endpoint() failed withstatus=20
Hello Tim, Thanks for the info. I also received this help from Myrinet: It looks like you are running out of endpoints. This discusses what endpoints are: http://www.myri.com/cgi-bin/fom.pl?file=421 And this explains how to increase the limit: http://www.myri.com/cgi-bin/fom.pl?file=482 Let us know if this doesn't address the problem. I haven't had time to look into it. -- Valmor > -Original Message- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > Behalf Of Tim Prins > Sent: Friday, March 30, 2007 10:49 PM > To: Open MPI Users > Subject: Re: [OMPI users] mca_btl_mx_init: mx_open_endpoint() failed > withstatus=20 > > Hi Valmor, > > What is happening here is that when Open MPI tries to create MX endpoint > for > communication, mx returns code 20, which is MX_BUSY. > > At this point we should gracefully move on, but there is a bug in Open MPI > 1.2 > which causes a segmentation fault in case of this type of error. This will > be > fixed in 1.2.1, and the fix is available now in the 1.2 nightly tarballs. > > Hope this helps, > > Tim > > On Friday 30 March 2007 05:06 pm, de Almeida, Valmor F. wrote: > > Hello, > > > > I am getting this error any time the number of processes requested per > > machine is greater than the number of cpus. I suspect it is something on > > the configuration of mx / ompi that I am missing since another machine I > > have without mx installed runs ompi correctly with oversubscription. > > > > Thanks for any help. > > > > -- > > Valmor > > > > > > ->mpirun -np 3 --machinefile mymachines-1 a.out > > [x1:23624] mca_btl_mx_init: mx_open_endpoint() failed with status=20 > > [x1:23624] *** Process received signal *** [x1:23624] Signal: > > Segmentation fault (11) [x1:23624] Signal code: Address not mapped (1) > > [x1:23624] Failing at address: 0x20 [x1:23624] [ 0] [0xb7f7f440] > > [x1:23624] [ 1] > > /opt/openmpi-1.2/lib/openmpi/mca_btl_mx.so(mca_btl_mx_finalize+0x25) > > [0xb7aca825] [x1:23624] [ 2] > > /opt/openmpi-1.2/lib/openmpi/mca_btl_mx.so(mca_btl_mx_component_init+0x6 > > f8) [0xb7acc658] [x1:23624] [ 3] > > /opt/ompi/lib/libmpi.so.0(mca_btl_base_select+0x1a0) [0xb7f41900] > > [x1:23624] [ 4] > > /opt/openmpi-1.2/lib/openmpi/mca_bml_r2.so(mca_bml_r2_component_init+0x2 > > 6) [0xb7ad1006] [x1:23624] [ 5] > > /opt/ompi/lib/libmpi.so.0(mca_bml_base_init+0x78) [0xb7f41198] > > [x1:23624] [ 6] > > /opt/openmpi-1.2/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_component_init+0 > > x7d) [0xb7af866d] [x1:23624] [ 7] > > /opt/ompi/lib/libmpi.so.0(mca_pml_base_select+0x176) [0xb7f49b56] > > [x1:23624] [ 8] /opt/ompi/lib/libmpi.so.0(ompi_mpi_init+0x4cf) > > [0xb7f0fe2f] [x1:23624] [ 9] /opt/ompi/lib/libmpi.so.0(MPI_Init+0xab) > > [0xb7f3204b] [x1:23624] [10] a.out(_ZN3MPI4InitERiRPPc+0x18) [0x8052cbe] > > [x1:23624] [11] a.out(main+0x21) [0x804f4a7] [x1:23624] [12] > > /lib/libc.so.6(__libc_start_main+0xdc) [0xb7be9824] > > > > content of mymachines-1 file > > > > x1 max_slots=4 > > > > > > > > ___ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
[OMPI users] mca_btl_mx_init: mx_open_endpoint() failed with status=20
Hello, I am getting this error any time the number of processes requested per machine is greater than the number of cpus. I suspect it is something on the configuration of mx / ompi that I am missing since another machine I have without mx installed runs ompi correctly with oversubscription. Thanks for any help. -- Valmor ->mpirun -np 3 --machinefile mymachines-1 a.out [x1:23624] mca_btl_mx_init: mx_open_endpoint() failed with status=20 [x1:23624] *** Process received signal *** [x1:23624] Signal: Segmentation fault (11) [x1:23624] Signal code: Address not mapped (1) [x1:23624] Failing at address: 0x20 [x1:23624] [ 0] [0xb7f7f440] [x1:23624] [ 1] /opt/openmpi-1.2/lib/openmpi/mca_btl_mx.so(mca_btl_mx_finalize+0x25) [0xb7aca825] [x1:23624] [ 2] /opt/openmpi-1.2/lib/openmpi/mca_btl_mx.so(mca_btl_mx_component_init+0x6 f8) [0xb7acc658] [x1:23624] [ 3] /opt/ompi/lib/libmpi.so.0(mca_btl_base_select+0x1a0) [0xb7f41900] [x1:23624] [ 4] /opt/openmpi-1.2/lib/openmpi/mca_bml_r2.so(mca_bml_r2_component_init+0x2 6) [0xb7ad1006] [x1:23624] [ 5] /opt/ompi/lib/libmpi.so.0(mca_bml_base_init+0x78) [0xb7f41198] [x1:23624] [ 6] /opt/openmpi-1.2/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_component_init+0 x7d) [0xb7af866d] [x1:23624] [ 7] /opt/ompi/lib/libmpi.so.0(mca_pml_base_select+0x176) [0xb7f49b56] [x1:23624] [ 8] /opt/ompi/lib/libmpi.so.0(ompi_mpi_init+0x4cf) [0xb7f0fe2f] [x1:23624] [ 9] /opt/ompi/lib/libmpi.so.0(MPI_Init+0xab) [0xb7f3204b] [x1:23624] [10] a.out(_ZN3MPI4InitERiRPPc+0x18) [0x8052cbe] [x1:23624] [11] a.out(main+0x21) [0x804f4a7] [x1:23624] [12] /lib/libc.so.6(__libc_start_main+0xdc) [0xb7be9824] content of mymachines-1 file x1 max_slots=4
[OMPI users] very long linking time with mixed-language libraries
Hello, I am using mpic++ to create a program that combines c++ and f90 libraries. The libraries are created with mpic++ and mpif90. OpenMPI-1.2 was built using gcc-4.1.1. (below follows the output of ompi_info. The final linking stage takes quite a long time compared to the creation of the libraries; I am wondering why and whether there is a way to speed up. Thanks for any inputs. -- Valmor ->./ompi_info Open MPI: 1.2 Open MPI SVN revision: r14027 Open RTE: 1.2 Open RTE SVN revision: r14027 OPAL: 1.2 OPAL SVN revision: r14027 Prefix: /usr/local/openmpi-1.2 Configured architecture: i686-pc-linux-gnu Configured by: root Configured on: Sun Mar 18 23:47:21 EDT 2007 Configure host: xeon0 Built by: root Built on: Sun Mar 18 23:57:41 EDT 2007 Built host: xeon0 C bindings: yes C++ bindings: yes Fortran77 bindings: yes (all) Fortran90 bindings: yes Fortran90 bindings size: medium C compiler: cc C compiler absolute: /usr/bin/cc C++ compiler: g++ C++ compiler absolute: /usr/bin/g++ Fortran77 compiler: gfortran Fortran77 compiler abs: /usr/i686-pc-linux-gnu/gcc-bin/4.1.1/gfortran Fortran90 compiler: gfortran Fortran90 compiler abs: /usr/i686-pc-linux-gnu/gcc-bin/4.1.1/gfortran C profiling: yes C++ profiling: yes Fortran77 profiling: yes Fortran90 profiling: yes C++ exceptions: no Thread support: posix (mpi: no, progress: no) Internal debug support: no MPI parameter check: always Memory profiling support: no Memory debugging support: no libltdl support: yes Heterogeneous support: yes mpirun default --prefix: no MCA backtrace: execinfo (MCA v1.0, API v1.0, Component v1.2) MCA memory: ptmalloc2 (MCA v1.0, API v1.0, Component v1.2) MCA paffinity: linux (MCA v1.0, API v1.0, Component v1.2) MCA maffinity: first_use (MCA v1.0, API v1.0, Component v1.2) MCA timer: linux (MCA v1.0, API v1.0, Component v1.2) MCA allocator: basic (MCA v1.0, API v1.0, Component v1.0) MCA allocator: bucket (MCA v1.0, API v1.0, Component v1.0) MCA coll: basic (MCA v1.0, API v1.0, Component v1.2) MCA coll: self (MCA v1.0, API v1.0, Component v1.2) MCA coll: sm (MCA v1.0, API v1.0, Component v1.2) MCA coll: tuned (MCA v1.0, API v1.0, Component v1.2) MCA io: romio (MCA v1.0, API v1.0, Component v1.2) MCA mpool: sm (MCA v1.0, API v1.0, Component v1.2) MCA pml: cm (MCA v1.0, API v1.0, Component v1.2) MCA pml: ob1 (MCA v1.0, API v1.0, Component v1.2) MCA bml: r2 (MCA v1.0, API v1.0, Component v1.2) MCA rcache: rb (MCA v1.0, API v1.0, Component v1.2) MCA rcache: vma (MCA v1.0, API v1.0, Component v1.2) MCA btl: self (MCA v1.0, API v1.0.1, Component v1.2) MCA btl: sm (MCA v1.0, API v1.0.1, Component v1.2) MCA btl: tcp (MCA v1.0, API v1.0.1, Component v1.0) MCA topo: unity (MCA v1.0, API v1.0, Component v1.2) MCA osc: pt2pt (MCA v1.0, API v1.0, Component v1.2) MCA errmgr: hnp (MCA v1.0, API v1.3, Component v1.2) MCA errmgr: orted (MCA v1.0, API v1.3, Component v1.2) MCA errmgr: proxy (MCA v1.0, API v1.3, Component v1.2)
