search for: openmpi

After the 7.2 upgrade?boost-openmpi-1.53.0-25 was installed, along with?openmpi-1.10.0-10. ?The old openmpi was then replaced with?compat- openmpi16-1.6.4-10. ?All fine. Except boost-openmpi has a dependency on the old libmpi.so.1 and the new openmpi has libmpi.so.12: # ldd libboost_mpi-mt.so.1.53.0? linux-vdso.so.1 =>??(0x00...

Just wondering if anyone can shed some light into an issue we are having with compat-openmpi after upgrading CentOS to version 6.5 Some of our cluster applications are dependent on an older version of OpenMPI, so we are using compat-openmpi. Up to CentOS 6.4 this was version 1.4.3: % /usr/lib64/compat-openmpi/bin/mpirun -V mpirun (Open MPI) 1.4.3 but after the upgrade to CentOS 6.5 it...

Sorry to take so long to reply ... On Thu, 2015-12-17 at 11:53 -0500, Tony Schreiner wrote: > Did you load the compat-openmpi environment module? > > module load mpi/compat-openmpi16-x86_64 Yes, but you can't load both mpi/openmpi-x86_64 and?mpi/compat- openmpi16-x86_64 as they are labelled as conflicting. As I said, if you load just mpi/compat-openmpi16-x86_64 it can't find the boost-openmpi library; if...

Hello, I try to install pbdMPI. Compilation successful, but load fails with segfault. Is anyone can help me? R version 3.0.0 pbdMPI version 0.1-6 Intel compiler version 13.1.1 OpenMPI version 1.6.4-1 CPU Intel x86_64 # R CMD INSTALL pbdMPI_0.1-6.tar.gz .. .... checking for gcc... icc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no...

Hi guys, I've spent a few days trying to install Rmpi with no luck. I originally tried using mpich, moved on to mpich2, and then to openmpi. I've gotten the furthest with openmpi, though am still running into this problem and can't figure it out. Can someone help!? Thanks so much in advanced. I'm using an HP Envy laptop with Ubuntu 12.04. Output is below, with the error at the bottom. link at Ubuntu12-04:~/Downloads$ R C...

I am trying to install the R package "Rmpi" which needs libmpi. I've installed openmpi and lam in Centos 5.2: [root at rab45-1 /]# rpm -qv openmpi openmpi-1.2.5-5.el5 openmpi-1.2.5-5.el5 [root at rab45-1 /]# rpm -qv lam lam-7.1.2-14.el5 lam-7.1.2-14.el5 But I get the following error message when trying to install Rmpi: /usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.so...

Did you load the compat-openmpi environment module? module load mpi/compat-openmpi16-x86_64 Tony On Thu, Dec 17, 2015 at 10:57 AM, Pete Biggs <pete at biggs.org.uk> wrote: > > After the 7.2 upgrade boost-openmpi-1.53.0-25 was installed, along > with openmpi-1.10.0-10. The old openmpi was then replaced with co...

Greetings. I see a warning message while compiling OpenMPI and would appreciate it if you tell me what it means. This warning happens with any OpenMPI > 1.6.5. Even before starting a cluster, just "sessionInfo" triggers this warning. I'm pasting in the message from R-3.3.2 (this is MRO). Do the R parallel package cluster functions viol...

...i so that I may take advantage of all of the CPUs in my computer, but I cannot get it to install and I am not very good with linux so it is adding to the headache. I have looked through the help archive, but I have not been successful at getting Rmpi to work. I am not sure if I am even installing openMPI correctly in linux. I would really like to get Rmpi to work so that I can take advantage of libraries that use Rmpi and more importantly reduce my computation time from several days to maybe a day. I am using fedora 11 (64-bit) on a AMD phenom III (AM3) system and I am not an expert at linux so I...

Hi list, It appears there is a problem with the OpenMPI I/O library on CentOS 6.2 & 6.3 (package openmpi-1.5.4-1.el6.x86_64). When I compile the attached program it ends up in the error path since MPI_File_open returns 16. The corresponding (unhelpful) message is: MPI_ERR_OTHER: known error not in list I couldn't find any pointers on the net...

...unce-request at centos.org You can reach the person managing the list at centos-announce-owner at centos.org When replying, please edit your Subject line so it is more specific than "Re: Contents of CentOS-announce digest..." Today's Topics: 1. CEBA-2008:0925 CentOS 4 x86_64 openmpi Update (Johnny Hughes) 2. CEBA-2008:0925 CentOS 4 i386 openmpi Update (Johnny Hughes) ---------------------------------------------------------------------- Message: 1 Date: Wed, 08 Oct 2008 06:01:19 -0500 From: Johnny Hughes <johnny at centos.org> Subject: [CentOS-announce] CEBA-2008:...

Hi folks, While building openmpi.4.0.0(Optimized debug build), using trunk clang we encountered a crash(assertion failure). Initially assertion seems trivial: [...] void llvm::DwarfExpression::addFragmentOffset(const llvm::DIExpression*): Assertion `FragmentOffset >= OffsetInBits && "overlapping or duplicate fragm...

CentOS Errata and Bugfix Advisory 2008:0925 Upstream details at : https://rhn.redhat.com/errata/RHBA-2008-0925.html The following updated files have been uploaded and are currently syncing to the mirrors: x86_64: openmpi11-1.1.5-1.el4_7.i386.rpm openmpi11-1.1.5-1.el4_7.x86_64.rpm openmpi-1.2.7-2.el4_7.i386.rpm openmpi-1.2.7-2.el4_7.x86_64.rpm openmpi-devel-1.2.7-2.el4_7.i386.rpm openmpi-devel-1.2.7-2.el4_7.x86_64.rpm openmpi-libs-1.2.7-2.el4_7.i386.rpm openmpi-libs-1.2.7-2.el4_7.x86_64.rpm src: openmpi11-1.1.5-1.e...

...n the r-help list in which people claim this should work: CC=mpicc R CMD INSTALL ... but it doesn't make a difference for me. The compiler that gets used is gcc, no matter how many different ways I try to say it should be mpicc: $ CC=mpicc R CMD INSTALL --configure-args=--with-mpi=/usr/lib64/openmpi/1.2.7-gcc --configure-vars=CC=mpicc Rmpi_0.5-8.tar.gz Password: * installing to library '/share/apps/lib/R/site-library' * installing *source* package 'Rmpi' ... checking for gcc... gcc -m64 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C...

Dear knowledgeable experts :-), I am trying to get openmpi, Rmpi and SNOW running on a Myrinet/GM cluster. I'm not an IT expert, but I surely could use a working installation of Rmpi and SNOW. I try to load the Rmpi library and get the following: > library(Rmpi) [master:07230] mca: base: component_find: unable to open osc pt2pt: file not foun...

...p://llvm.org/bugs/show_bug.cgi?id=11756 I believe the bug I am reporting is already reported in bug # 11969 when building FreeBSD world: http://llvm.org/bugs/show_bug.cgi?id=11969 --- To reproduce the problem: Program I am compiling: http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.3.tar.bz2 Version of LLVM/Clang: 3.1 How I compiled LLVM: # \see llvm.org/docs/Packaging.html ../llvm-3.1.src/configure \ --prefix=/software/compilers/llvm/3.1 \ --disable-assertions \ --enable-debug-symbols \ --enable-optimized \ --enable-shared \ make -j 4 make install Command genera...

Hi all, I'm using RScalapack library for parallelizing some heavy matrix operations required by MCMC methods for spatio-temporal models. The package reference manuals (dated 2005) states that the library needs LamMPI to work but we have a Linux Cluster with OpenMPI. We have found (http://cvs.fedoraproject.org/viewvc/devel/R-RScaLAPACK/) a patch for OpenMPI but we are wondering if in the meanwhile the package has been compiled also for OpenMPI. Does anybody use RScalapack and has any suggestions? Sorry for writing here but nobody answered in the R-sig- hpc (H...

...the r-help list in which people claim this should work: CC=mpicc R CMD INSTALL ... but it doesn't make a difference for me. The compiler that gets used is gcc, no matter how many different ways I try to say it should be mpicc: $ CC=mpicc R CMD INSTALL --configure-args=--with-mpi=/usr/lib64/openmpi/1.2.7-gcc --configure-vars=CC=mpicc Rmpi_0.5-8.tar.gz Password: * installing to library '/share/apps/lib/R/site-library' * installing *source* package 'Rmpi' ... checking for gcc... gcc -m64 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C...

I'm running R/snow on a small cluster with opensuse, openmpi, and openshh. I start up R with "mpirun -n 1 R --no-save". That works but it strikes me how easily I get kicked out of R whenever I run into syntax errors. Is there a way to avoid this, for instance, by starting up a regular R session and invoking/activating(?) openmpi within R, e.g. by p...

Hello, I plan to use R with my cluster with OpenMPI. I need the packaged 'snow' and 'Rmpi' for that, however, I get an error while downloading and installing them: When I do a: install.packages("Rmpi", dependencies=T) I get this error: checking for mpi.h... no Try to find libmpi.so or libmpich.a checking fo...