October 2013 - discuss - mailman3.cels.anl.gov

help compiling WRF model using intel compilers and mpich
by Alen Arturo Dioses Avellaneda 17 Oct '13

17 Oct '13

Hello, I am sorry because this is not topic of te group, but maybe anyone could help me. I am trying to compile WRFmodel 3.4.1 using intel compilers (v 13.1.3) and MPICH-1.2.7p1. I had use intel compilers and mpich for BRAMS (Brazilian development on the Atmosferic Modeling System) model and works well. Frist, I had problems instaling netcdf 4.2 libraries, so I used netcdf 3.6.3 and compile without problems. The configure script works well but the compile script does not. I am sendin the compile.log document. Information about my PC, I have four processors Intel (R) Xeon (TM) CPU 3.06Hz, CentOS 5.9, uname -a (Linux localhost.localdomain 2.6.18-348.6.1.el5 #1 SMP Tue May 21 15:34:22 EDT 2013 i686 i686 i386 GNU/Linux). Also I use ssh conection without password. Information about the libraries, I compile the following libraries. ($STUFF=/home/Alen/brams/stuff) intel compilers were compiler in /opt/intel jpeg v6b: CC=icc ./configure –-prefix=$STUFF Make Make install Make install-lib zlib-1.1.4 CC=icc ./configure – prefix=$STUFF Make Make install HDF4 v4.2r0 F77=ifort CC=icc ./configure –prefix=$STUFF –with-jpeg=$STUFF –with-zlib=$STUFF Make Make install Mpich-1.2.7p1 RSHCOMMAND=ssh FC=ifort F77=ifort F90=ifort CC=icc CXX=icpc ./configure --prefix=$STUFF Make Make install Netcdf 3.6.3 export F77=ifort export FC=ifort export F90=ifort export CC=icc export CXX=icpc ./configure --prefix=/usr/local/netcdf make make check make install Finally, I want to thank you for any advice or help you can give me.

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Re: [mpich-discuss] mpich - siesta - cluster
by Julio Henrique 15 Oct '13

15 Oct '13

Regarding dependencies is fine. My question was only about the Siesta. Thank so much, Jeff and Pavan. Julio. > From: balaji(a)mcs.anl.gov > Date: Tue, 15 Oct 2013 18:19:22 -0500 > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] mpich - siesta - cluster > > > The safest way is to build mpich on an shared file system (e.g., NFS) that is mounted on all nodes. If that's not available, then just install mpich on all nodes. > > You can be a little more brave to actually figure out the library dependencies like Jeff suggested, if you really care to. But installing on all machines will be safe either way. > > -- Pavan > > On Oct 15, 2013, at 6:14 PM, Julio Henrique wrote: > > > Yes Jeff, I read your previous email. > > I was just taking the doubt. > > So, I just build everything there, i.e., libraries and siesta on all nodes and server. > > Is it? > > If not, forgive me, my english is not good. > > Thanks Jeff. > > Julio. > > > > > > > > > > > > > > From: jeff.science(a)gmail.com > > Date: Tue, 15 Oct 2013 17:31:15 -0500 > > To: discuss(a)mpich.org > > Subject: Re: [mpich-discuss] mpich - siesta - cluster > > > > Did you read my previous email? > > > > Jeff > > > > On Tue, Oct 15, 2013 at 5:16 PM, Julio Henrique <juliohenrique(a)msn.com> wrote: > > I have mpich-3.0.4 compiled with > > # ./configure --prefix=/opt/mpich --enable-shared --enable-f95 --enable-threads=runtime --enable-romio --enable-nemesis-shm-collectives --with-pvfs2=/opt/pvfs2 --with-file-system="pvfs2+nfs" --with-thread-package=posix --with-device=ch3:nemesis --with-java=/etc/java-7-openjdk > > # make > > # make install > > > > and PVFS2 on Whezzy 7.2 and works fine. > > 01 server and 08 nodes. > > > > However, I want to install Siesta and my doubt is: I need to install Siesta on all nodes AND on server or just on server? > > > > Thank's. > > Julio. > > > > > > > > > > > > > > > > > > From: jeff.science(a)gmail.com > > Date: Tue, 15 Oct 2013 15:55:44 -0500 > > To: discuss(a)mpich.org > > Subject: Re: [mpich-discuss] mpich - siesta - cluster > > > > > > If you use a static binary, you don't need the libraries to live on the compute nodes. If you use a binary with dynamic linkage (run 'ldd binary.x' to see what the dependencies are), then you need those paths to resolve everywhere the binary launches. > > > > If you have a shared filesystem, just build everything there. > > > > Jeff > > > > On Tue, Oct 15, 2013 at 3:52 PM, Julio Henrique <juliohenrique(a)msn.com> wrote: > > Does anyone know if I need to install the Siesta (ab initio molecular dynamics simulations ) only on the server or on all nodes in a cluster? > > Or just a libraries (mpich, blacs, scalapck, etc) on nodes and the libraries and Siesta on the server? > > Julio. > > > > > > > > > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > > > -- > > Jeff Hammond > > jeff.science(a)gmail.com > > > > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > > > -- > > Jeff Hammond > > jeff.science(a)gmail.com > > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] mpich - siesta - cluster
by Pavan Balaji 15 Oct '13

15 Oct '13

The safest way is to build mpich on an shared file system (e.g., NFS) that is mounted on all nodes. If that's not available, then just install mpich on all nodes. You can be a little more brave to actually figure out the library dependencies like Jeff suggested, if you really care to. But installing on all machines will be safe either way. -- Pavan On Oct 15, 2013, at 6:14 PM, Julio Henrique wrote: > Yes Jeff, I read your previous email. > I was just taking the doubt. > So, I just build everything there, i.e., libraries and siesta on all nodes and server. > Is it? > If not, forgive me, my english is not good. > Thanks Jeff. > Julio. > > > > > > > From: jeff.science(a)gmail.com > Date: Tue, 15 Oct 2013 17:31:15 -0500 > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] mpich - siesta - cluster > > Did you read my previous email? > > Jeff > > On Tue, Oct 15, 2013 at 5:16 PM, Julio Henrique <juliohenrique(a)msn.com> wrote: > I have mpich-3.0.4 compiled with > # ./configure --prefix=/opt/mpich --enable-shared --enable-f95 --enable-threads=runtime --enable-romio --enable-nemesis-shm-collectives --with-pvfs2=/opt/pvfs2 --with-file-system="pvfs2+nfs" --with-thread-package=posix --with-device=ch3:nemesis --with-java=/etc/java-7-openjdk > # make > # make install > > and PVFS2 on Whezzy 7.2 and works fine. > 01 server and 08 nodes. > > However, I want to install Siesta and my doubt is: I need to install Siesta on all nodes AND on server or just on server? > > Thank's. > Julio. > > > > > > > > > From: jeff.science(a)gmail.com > Date: Tue, 15 Oct 2013 15:55:44 -0500 > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] mpich - siesta - cluster > > > If you use a static binary, you don't need the libraries to live on the compute nodes. If you use a binary with dynamic linkage (run 'ldd binary.x' to see what the dependencies are), then you need those paths to resolve everywhere the binary launches. > > If you have a shared filesystem, just build everything there. > > Jeff > > On Tue, Oct 15, 2013 at 3:52 PM, Julio Henrique <juliohenrique(a)msn.com> wrote: > Does anyone know if I need to install the Siesta (ab initio molecular dynamics simulations ) only on the server or on all nodes in a cluster? > Or just a libraries (mpich, blacs, scalapck, etc) on nodes and the libraries and Siesta on the server? > Julio. > > > > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > > > -- > Jeff Hammond > jeff.science(a)gmail.com > > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > > > -- > Jeff Hammond > jeff.science(a)gmail.com > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] mpich - siesta - cluster
by Julio Henrique 15 Oct '13

15 Oct '13

Yes Jeff, I read your previous email. I was just taking the doubt. So, I just build everything there, i.e., libraries and siesta on all nodes and server. Is it? If not, forgive me, my english is not good. Thanks Jeff. Julio. From: jeff.science(a)gmail.com Date: Tue, 15 Oct 2013 17:31:15 -0500 To: discuss(a)mpich.org Subject: Re: [mpich-discuss] mpich - siesta - cluster Did you read my previous email? Jeff On Tue, Oct 15, 2013 at 5:16 PM, Julio Henrique <juliohenrique(a)msn.com> wrote: I have mpich-3.0.4 compiled with # ./configure --prefix=/opt/mpich --enable-shared --enable-f95 --enable-threads=runtime --enable-romio --enable-nemesis-shm-collectives --with-pvfs2=/opt/pvfs2 --with-file-system="pvfs2+nfs" --with-thread-package=posix --with-device=ch3:nemesis --with-java=/etc/java-7-openjdk # make # make install and PVFS2 on Whezzy 7.2 and works fine. 01 server and 08 nodes. However, I want to install Siesta and my doubt is: I need to install Siesta on all nodes AND on server or just on server? Thank's. Julio. From: jeff.science(a)gmail.com Date: Tue, 15 Oct 2013 15:55:44 -0500 To: discuss(a)mpich.org Subject: Re: [mpich-discuss] mpich - siesta - cluster If you use a static binary, you don't need the libraries to live on the compute nodes. If you use a binary with dynamic linkage (run 'ldd binary.x' to see what the dependencies are), then you need those paths to resolve everywhere the binary launches. If you have a shared filesystem, just build everything there. Jeff On Tue, Oct 15, 2013 at 3:52 PM, Julio Henrique <juliohenrique(a)msn.com> wrote: Does anyone know if I need to install the Siesta (ab initio molecular dynamics simulations ) only on the server or on all nodes in a cluster? Or just a libraries (mpich, blacs, scalapck, etc) on nodes and the libraries and Siesta on the server? Julio. _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond jeff.science(a)gmail.com _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond jeff.science(a)gmail.com _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] mpich - siesta - cluster
by Jeff Hammond 15 Oct '13

15 Oct '13

Did you read my previous email? Jeff On Tue, Oct 15, 2013 at 5:16 PM, Julio Henrique <juliohenrique(a)msn.com>wrote: > I have mpich-3.0.4 compiled with > # ./configure --prefix=/opt/mpich --enable-shared --enable-f95 > --enable-threads=runtime --enable-romio --enable-nemesis-shm-collectives > --with-pvfs2=/opt/pvfs2 --with-file-system="pvfs2+nfs" > --with-thread-package=posix --with-device=ch3:nemesis > --with-java=/etc/java-7-openjdk > # make > # make install > > and PVFS2 on Whezzy 7.2 and works fine. > 01 server and 08 nodes. > > However, I want to install Siesta and my doubt is: I need to install > Siesta on all nodes AND on server or just on server? > > Thank's. > Julio. > > > > > > > > > > ------------------------------ > From: jeff.science(a)gmail.com > Date: Tue, 15 Oct 2013 15:55:44 -0500 > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] mpich - siesta - cluster > > > If you use a static binary, you don't need the libraries to live on the > compute nodes. If you use a binary with dynamic linkage (run 'ldd > binary.x' to see what the dependencies are), then you need those paths to > resolve everywhere the binary launches. > > If you have a shared filesystem, just build everything there. > > Jeff > > On Tue, Oct 15, 2013 at 3:52 PM, Julio Henrique <juliohenrique(a)msn.com>wrote: > > Does anyone know if I need to install the Siesta (ab initio molecular > dynamics simulations ) only on the server or on all nodes in a cluster? > Or just a libraries (mpich, blacs, scalapck, etc) on nodes and the > libraries and Siesta on the server? > Julio. > > > > > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > > > > -- > Jeff Hammond > jeff.science(a)gmail.com > > _______________________________________________ discuss mailing list > discuss(a)mpich.org To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- Jeff Hammond jeff.science(a)gmail.com

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Re: [mpich-discuss] mpich - siesta - cluster
by Julio Henrique 15 Oct '13

15 Oct '13

I have mpich-3.0.4 compiled with # ./configure --prefix=/opt/mpich --enable-shared --enable-f95 --enable-threads=runtime --enable-romio --enable-nemesis-shm-collectives --with-pvfs2=/opt/pvfs2 --with-file-system="pvfs2+nfs" --with-thread-package=posix --with-device=ch3:nemesis --with-java=/etc/java-7-openjdk # make # make install and PVFS2 on Whezzy 7.2 and works fine. 01 server and 08 nodes. However, I want to install Siesta and my doubt is: I need to install Siesta on all nodes AND on server or just on server? Thank's. Julio. From: jeff.science(a)gmail.com Date: Tue, 15 Oct 2013 15:55:44 -0500 To: discuss(a)mpich.org Subject: Re: [mpich-discuss] mpich - siesta - cluster If you use a static binary, you don't need the libraries to live on the compute nodes. If you use a binary with dynamic linkage (run 'ldd binary.x' to see what the dependencies are), then you need those paths to resolve everywhere the binary launches. If you have a shared filesystem, just build everything there. Jeff On Tue, Oct 15, 2013 at 3:52 PM, Julio Henrique <juliohenrique(a)msn.com> wrote: Does anyone know if I need to install the Siesta (ab initio molecular dynamics simulations ) only on the server or on all nodes in a cluster? Or just a libraries (mpich, blacs, scalapck, etc) on nodes and the libraries and Siesta on the server? Julio. _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond jeff.science(a)gmail.com _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] mpich - siesta - cluster
by Jeff Hammond 15 Oct '13

15 Oct '13

If you use a static binary, you don't need the libraries to live on the compute nodes. If you use a binary with dynamic linkage (run 'ldd binary.x' to see what the dependencies are), then you need those paths to resolve everywhere the binary launches. If you have a shared filesystem, just build everything there. Jeff On Tue, Oct 15, 2013 at 3:52 PM, Julio Henrique <juliohenrique(a)msn.com>wrote: > Does anyone know if I need to install the Siesta (ab initio molecular > dynamics simulations ) only on the server or on all nodes in a cluster? > Or just a libraries (mpich, blacs, scalapck, etc) on nodes and the > libraries and Siesta on the server? > Julio. > > > > > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- Jeff Hammond jeff.science(a)gmail.com

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mpich - siesta - cluster
by Julio Henrique 15 Oct '13

15 Oct '13

Does anyone know if I need to install the Siesta (ab initio molecular dynamics simulations ) only on the server or on all nodes in a cluster? Or just a libraries (mpich, blacs, scalapck, etc) on nodes and the libraries and Siesta on the server? Julio.

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Re: [mpich-discuss] Bugs in Hydra-KVS
by Ken Raffenetti 14 Oct '13

14 Oct '13

Hi Jan, Thanks for reporting this. I will review your patches and apply them soon. Thanks, Ken ----- Original Message ----- > From: "Jan Bierbaum" <jan.bierbaum(a)tudos.org> > To: discuss(a)mpich.org > Sent: Monday, October 14, 2013 4:47:28 AM > Subject: [mpich-discuss] Bugs in Hydra-KVS > > Hello! > > > Doing some experiments with an older version of MPICH I stumbled upon > two bugs in 'HYD_pmcd_pmi_add_kvs', both of which are still present > according to Git [1]: > > The loop traverses all KVS entries and checks for one with a > duplicate > key. However, it will not check the last entry (Bug 1). When a > duplicate > entry is found the loop is aborted. But the newly created 'key_pair' > is > never freed (Bug 2). I attached a patch that fixes both issues. > > Also, newer versions of MPICH do not check anymore whether a > duplicate > KVS entry was encountered - 'HYD_status fn_put' ignores 'ret' > completely > [2] whereas it did some error checking and reporting in older > versions. > This change was introduced in commit > b98c7fd361541659d7e8fb6ef7fc76547024ad75 [3] and I am not sure > whether > this check was removed intentionally or rather by accident. > > Last but not least the README in the release tarball is a bit > outdated > and still refers to the old site, mailing list and SVN repository. I > attach another patch that updates the file. I also propose to add a > link > to the Git Wiki page [4] directly at the end of the download page > [5]. > It took me quiet a while to realize the repository was publicly > available. > > > > Regards, Jan > > > [1] > http://git.mpich.org/mpich.git/blob/HEAD:/src/pm/hydra/pm/pmiserv/common.c#… > [2] > http://git.mpich.org/mpich.git/blob/HEAD:/src/pm/hydra/pm/pmiserv/pmiserv_p… > [3] > http://git.mpich.org/mpich.git/commit/b98c7fd361541659d7e8fb6ef7fc76547024a… > [4] https://wiki.mpich.org/mpich/index.php/Getting_And_Building_MPICH > [5] https://www.mpich.org/downloads/ > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] new communicator value differs for myid=0
by Shan-ho Tsai 14 Oct '13

14 Oct '13

Hi Rajeev, Thank you so much for the clarification, I really appreciate it. Regards, Shan-Ho ________________________________________ From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Rajeev Thakur [thakur(a)mcs.anl.gov] Sent: Monday, October 14, 2013 4:02 PM To: discuss(a)mpich.org Subject: Re: [mpich-discuss] new communicator value differs for myid=0 The communicator is an opaque object. The value of the new communicator variable is not useful. It is a local variable and can be different on each process. As long as the new communicator behaves the way it should, the program is ok. Rajeev On Oct 14, 2013, at 2:50 PM, Shan-ho Tsai wrote: > > Hello, > I am using MPICH2 3.0.2 with gfortran 4.4.7 on a 64-bit > Linux machine. The program uses MPI_Comm_split to > create a new communicator. All processes print the same > value for MPI_COMM_WORLD, but for the new communicator, > all processes with myid greater than zero print the same value, > but myid=0 prints a different value. Why is that? I thought > all processes should print the same number as well. > > Simple test code: > =================================================== > PROGRAM Test > IMPLICIT NONE > include "mpif.h" > INTEGER :: nBins=8, nWalkers=8 > INTEGER :: ierr,numprocs,myid,energy_comm > INTEGER :: energy_id,numranks,iBin,iWalker > INTEGER :: mpistatus(MPI_STATUS_SIZE) > > CALL MPI_INIT(ierr) > CALL MPI_COMM_SIZE(MPI_COMM_WORLD,numprocs,ierr) > CALL MPI_COMM_RANK(MPI_COMM_WORLD,myid,ierr) > > iBin = myid/nWalkers > iWalker = MOD(myid,nWalkers) > CALL MPI_Comm_split(MPI_COMM_WORLD,iBin,iWalker,energy_comm,ierr) > CALL MPI_COMM_SIZE(energy_comm,numranks,ierr) > CALL MPI_COMM_RANK(energy_comm,energy_id,ierr) > > write(*,*)myid,MPI_COMM_WORLD,energy_comm > > CALL MPI_FINALIZE(ierr) > > END PROGRAM Test > ========================================================= > > Compile with > > mpif90 test.f90 > > Run with > > mpirun -n 4 -f host.txt ./a.out > > Generates > 0 1140850688 -2080374780 > 2 1140850688 -2080374782 > 1 1140850688 -2080374782 > 3 1140850688 -2080374782 > > "mpif90 -v" returns: > > mpif90 for MPICH version 3.0.2 > Using built-in specs. > Target: x86_64-redhat-linux6E > Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --disable-gnu-unique-object --with-as=/usr/libexec/binutils220/as --enable-languages=c,c++,fortran --disable-libgcj --with-mpfr=/builddir/build/BUILD/gcc-4.4.7-20120601/obj-x86_64-redhat-linux6E/mpfr-install/ --with-ppl=/builddir/build/BUILD/gcc-4.4.7-20120601/obj-x86_64-redhat-linux6E/ppl-install --with-cloog=/builddir/build/BUILD/gcc-4.4.7-20120601/obj-x86_64-redhat-linux6E/cloog-install --with-tune=generic --with-arch_32=i586 --build=x86_64-redhat-linux6E > Thread model: posix > gcc version 4.4.7 20120313 (Red Hat 4.4.7-1) (GCC) > > I get the same output for MPICH2 1.4.1p1. > Any ideas what is happening? Or shouldn't the new communicator also > have the same value for all myids? > > Thank you very much for any suggestions. > Shan-Ho > > ---------------------------------------------------- > Shan-Ho Tsai > University of Georgia > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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