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

Re: [mpich-discuss] Configuration issues for mpich2-1.5b2
by Dave Goodell 29 Jan '13

29 Jan '13

On Jan 29, 2013, at 8:14 AM CST, Bharath Ramesh wrote: > On Tue, Jan 29, 2013 at 08:08:29AM -0600, Dave Goodell wrote: >> The relevant config.log files would help here. You can grab all of them for us with: >> >> find . -name "config.log" | xargs tar czf config.logs.tar.gz >> >> from your build directory. Then just send us "config.logs.tar.gz". > > I have attached the tar ball of all the config.log from the build > directory. Your LD_LIBRARY_PATH (or other library path configuration mechanism) is configured incorrectly: ----8<---- configure:16164: checking size of void * configure:16169: gcc -o conftest -O2 -I/home/bramesh/ARC/apps/build/mpich-3.0.1/src/mpl/include -I/home/bramesh/ARC/apps/build/mpich-3.0.1/src/mpl/include -I/home/bramesh/ARC/apps/build/mpich-3.0.1/src/openpa/src -I/home/bramesh/ARC/apps/build/mpich-3.0.1/src/openpa/src -I/home/bramesh/ARC/apps/build/mpich-3.0.1/src/mpi/romio/include -I/opt/torque/torque/include -lnsl -L/opt/torque/torque/lib64 -L/opt/torque/torque/lib conftest.c -ltorque >&5 configure:16169: $? = 0 configure:16169: ./conftest ./conftest: error while loading shared libraries: libtorque.so.2: cannot open shared object file: No such file or directory configure:16169: $? = 127 configure: program exited with status 127 configure: failed program was: […] ----8<---- -Dave

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Re: [mpich-discuss] Configuration issues for mpich2-1.5b2
by Bharath Ramesh 29 Jan '13

29 Jan '13

On Tue, Jan 29, 2013 at 08:08:29AM -0600, Dave Goodell wrote: > The relevant config.log files would help here. You can grab all of them for us with: > > find . -name "config.log" | xargs tar czf config.logs.tar.gz > > from your build directory. Then just send us "config.logs.tar.gz". Going through hydra's config.log I see that for some reason hydra is unable to find libtroque.so.2 which is in the path. I am going to see if passing the path as part of CFLAGS or LDFLAGS is going to fix this issue for me. -- Bharath

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Re: [mpich-discuss] Configuration issues for mpich2-1.5b2
by Bharath Ramesh 29 Jan '13

29 Jan '13

On Tue, Jan 29, 2013 at 08:08:29AM -0600, Dave Goodell wrote: > The relevant config.log files would help here. You can grab all of them for us with: > > find . -name "config.log" | xargs tar czf config.logs.tar.gz > > from your build directory. Then just send us "config.logs.tar.gz". I have attached the tar ball of all the config.log from the build directory. -- Bharath

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Re: [mpich-discuss] Configuration issues for mpich2-1.5b2
by Dave Goodell 29 Jan '13

29 Jan '13

The relevant config.log files would help here. You can grab all of them for us with: find . -name "config.log" | xargs tar czf config.logs.tar.gz from your build directory. Then just send us "config.logs.tar.gz". -Dave On Jan 29, 2013, at 7:20 AM CST, Pavan Balaji wrote: > > Ah, the sizeof calculations? Nevermind. I'm looking into it. > > -- Pavan > > On 01/29/2013 07:17 AM US Central Time, Pavan Balaji wrote: >> >> What exactly is the error? I don't see it in the output you sent. >> Sorry if I missing something obvious here. >> >> -- Pavan >> >> On 01/29/2013 06:24 AM US Central Time, Bharath Ramesh wrote: >>> On 1/29/2013 12:28 AM, Dave Goodell wrote: >>>> Does the issue occur with the latest release of stock MPICH (3.0.1)? >>>> 1.5b2 was a beta release and there have been many fixes since then. >>> >>> I tried the latest mpich-3.0.1 and mpich2-1.5 and both give me the same >>> error. >>> >>> Output from 3.0.1: >>> >>> ### >>> ### Configuring hwloc core >>> ### >>> checking hwloc building mode... embedded >>> configure: hwloc builddir: >>> /home/bramesh/ARC/apps/build/mpich-3.0.1/src/pm/hydra/tools/topo/hwloc/hwloc >>> >>> configure: hwloc srcdir: >>> /home/bramesh/ARC/apps/build/mpich-3.0.1/src/pm/hydra/tools/topo/hwloc/hwloc >>> >>> checking if want hwloc maintainer support... disabled (embedded mode) >>> checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ >>> checking for hwloc symbol prefix... hwloc_ >>> checking size of void *... 0 >>> checking which OS support to include... Linux >>> checking which CPU support to include... unknown -- assuming x86_64 >>> checking size of unsigned long... (cached) 8 >>> checking size of unsigned int... 0 >>> checking for the C compiler vendor... gnu >>> >>> configure line: >>> ./configure --prefix=/home/bramesh/apps/mpich --enable-shared >>> --with-pbs=/opt/torque/torque >>> >>> Output from 1.5: >>> >>> ### >>> ### Configuring hwloc core >>> ### >>> checking hwloc building mode... embedded >>> configure: hwloc builddir: >>> /home/bramesh/ARC/apps/build/mpich2-1.5/src/pm/hydra/tools/topo/hwloc/hwloc >>> configure: hwloc srcdir: >>> /home/bramesh/ARC/apps/build/mpich2-1.5/src/pm/hydra/tools/topo/hwloc/hwloc >>> checking if want hwloc maintainer support... disabled (embedded mode) >>> checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ >>> checking for hwloc symbol prefix... hwloc_ >>> checking size of void *... 0 >>> checking which OS support to include... Linux >>> checking which CPU support to include... unknown -- assuming x86_64 >>> checking size of unsigned long... (cached) 8 >>> checking size of unsigned int... 0 >>> checking for the C compiler vendor... gnu >>> >>> configure line: >>> ./configure --prefix=/home/bramesh/apps/mpich2 --enable-shared >>> --with-pbs=/opt/torque/torque >>> >>> >>> >>> _______________________________________________ >>> 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] Configuration issues for mpich2-1.5b2
by Bharath Ramesh 29 Jan '13

29 Jan '13

On 1/29/2013 8:46 AM, Pavan Balaji wrote: > Bharath, > > I tried this with a variety of combinations: with and without torque, > with and without shared, and master and 3.0.1. But none of them seem to > show the problem you are having on x86_64/Linux. > > Can you give some more specifics on your system (i.e., what compiler, > what version, what Linux)? $ uname -a Linux brbuild 2.6.32-279.el6.x86_64 #1 SMP Fri Jun 22 12:19:21 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux $ cat /etc/issue CentOS release 6.3 (Final) Kernel \r on an \m $ gcc --version gcc (GCC) 4.5.3 Copyright (C) 2010 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. $ autoconf --version autoconf (GNU Autoconf) 2.63 Copyright (C) 2008 Free Software Foundation, Inc. License GPLv2+: GNU GPL version 2 or later <http://gnu.org/licenses/old-licenses/gpl-2.0.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Written by David J. MacKenzie and Akim Demaille. Hope this helps. -- Bharath

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Re: [mpich-discuss] Configuration issues for mpich2-1.5b2
by Pavan Balaji 29 Jan '13

29 Jan '13

Bharath, On 01/29/2013 06:24 AM US Central Time, Bharath Ramesh wrote: > Output from 3.0.1: > > ### > ### Configuring hwloc core > ### > checking hwloc building mode... embedded > configure: hwloc builddir: > /home/bramesh/ARC/apps/build/mpich-3.0.1/src/pm/hydra/tools/topo/hwloc/hwloc > > configure: hwloc srcdir: > /home/bramesh/ARC/apps/build/mpich-3.0.1/src/pm/hydra/tools/topo/hwloc/hwloc > > checking if want hwloc maintainer support... disabled (embedded mode) > checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ > checking for hwloc symbol prefix... hwloc_ > checking size of void *... 0 > checking which OS support to include... Linux > checking which CPU support to include... unknown -- assuming x86_64 > checking size of unsigned long... (cached) 8 > checking size of unsigned int... 0 > checking for the C compiler vendor... gnu > > configure line: > ./configure --prefix=/home/bramesh/apps/mpich --enable-shared > --with-pbs=/opt/torque/torque I tried this with a variety of combinations: with and without torque, with and without shared, and master and 3.0.1. But none of them seem to show the problem you are having on x86_64/Linux. Can you give some more specifics on your system (i.e., what compiler, what version, what Linux)? -- Pavan -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Configuration issues for mpich2-1.5b2
by Pavan Balaji 29 Jan '13

29 Jan '13

Ah, the sizeof calculations? Nevermind. I'm looking into it. -- Pavan On 01/29/2013 07:17 AM US Central Time, Pavan Balaji wrote: > > What exactly is the error? I don't see it in the output you sent. > Sorry if I missing something obvious here. > > -- Pavan > > On 01/29/2013 06:24 AM US Central Time, Bharath Ramesh wrote: >> On 1/29/2013 12:28 AM, Dave Goodell wrote: >>> Does the issue occur with the latest release of stock MPICH (3.0.1)? >>> 1.5b2 was a beta release and there have been many fixes since then. >> >> I tried the latest mpich-3.0.1 and mpich2-1.5 and both give me the same >> error. >> >> Output from 3.0.1: >> >> ### >> ### Configuring hwloc core >> ### >> checking hwloc building mode... embedded >> configure: hwloc builddir: >> /home/bramesh/ARC/apps/build/mpich-3.0.1/src/pm/hydra/tools/topo/hwloc/hwloc >> >> configure: hwloc srcdir: >> /home/bramesh/ARC/apps/build/mpich-3.0.1/src/pm/hydra/tools/topo/hwloc/hwloc >> >> checking if want hwloc maintainer support... disabled (embedded mode) >> checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ >> checking for hwloc symbol prefix... hwloc_ >> checking size of void *... 0 >> checking which OS support to include... Linux >> checking which CPU support to include... unknown -- assuming x86_64 >> checking size of unsigned long... (cached) 8 >> checking size of unsigned int... 0 >> checking for the C compiler vendor... gnu >> >> configure line: >> ./configure --prefix=/home/bramesh/apps/mpich --enable-shared >> --with-pbs=/opt/torque/torque >> >> Output from 1.5: >> >> ### >> ### Configuring hwloc core >> ### >> checking hwloc building mode... embedded >> configure: hwloc builddir: >> /home/bramesh/ARC/apps/build/mpich2-1.5/src/pm/hydra/tools/topo/hwloc/hwloc >> configure: hwloc srcdir: >> /home/bramesh/ARC/apps/build/mpich2-1.5/src/pm/hydra/tools/topo/hwloc/hwloc >> checking if want hwloc maintainer support... disabled (embedded mode) >> checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ >> checking for hwloc symbol prefix... hwloc_ >> checking size of void *... 0 >> checking which OS support to include... Linux >> checking which CPU support to include... unknown -- assuming x86_64 >> checking size of unsigned long... (cached) 8 >> checking size of unsigned int... 0 >> checking for the C compiler vendor... gnu >> >> configure line: >> ./configure --prefix=/home/bramesh/apps/mpich2 --enable-shared >> --with-pbs=/opt/torque/torque >> >> >> >> _______________________________________________ >> 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] Configuration issues for mpich2-1.5b2
by Pavan Balaji 29 Jan '13

29 Jan '13

What exactly is the error? I don't see it in the output you sent. Sorry if I missing something obvious here. -- Pavan On 01/29/2013 06:24 AM US Central Time, Bharath Ramesh wrote: > On 1/29/2013 12:28 AM, Dave Goodell wrote: >> Does the issue occur with the latest release of stock MPICH (3.0.1)? >> 1.5b2 was a beta release and there have been many fixes since then. > > I tried the latest mpich-3.0.1 and mpich2-1.5 and both give me the same > error. > > Output from 3.0.1: > > ### > ### Configuring hwloc core > ### > checking hwloc building mode... embedded > configure: hwloc builddir: > /home/bramesh/ARC/apps/build/mpich-3.0.1/src/pm/hydra/tools/topo/hwloc/hwloc > > configure: hwloc srcdir: > /home/bramesh/ARC/apps/build/mpich-3.0.1/src/pm/hydra/tools/topo/hwloc/hwloc > > checking if want hwloc maintainer support... disabled (embedded mode) > checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ > checking for hwloc symbol prefix... hwloc_ > checking size of void *... 0 > checking which OS support to include... Linux > checking which CPU support to include... unknown -- assuming x86_64 > checking size of unsigned long... (cached) 8 > checking size of unsigned int... 0 > checking for the C compiler vendor... gnu > > configure line: > ./configure --prefix=/home/bramesh/apps/mpich --enable-shared > --with-pbs=/opt/torque/torque > > Output from 1.5: > > ### > ### Configuring hwloc core > ### > checking hwloc building mode... embedded > configure: hwloc builddir: > /home/bramesh/ARC/apps/build/mpich2-1.5/src/pm/hydra/tools/topo/hwloc/hwloc > configure: hwloc srcdir: > /home/bramesh/ARC/apps/build/mpich2-1.5/src/pm/hydra/tools/topo/hwloc/hwloc > checking if want hwloc maintainer support... disabled (embedded mode) > checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ > checking for hwloc symbol prefix... hwloc_ > checking size of void *... 0 > checking which OS support to include... Linux > checking which CPU support to include... unknown -- assuming x86_64 > checking size of unsigned long... (cached) 8 > checking size of unsigned int... 0 > checking for the C compiler vendor... gnu > > configure line: > ./configure --prefix=/home/bramesh/apps/mpich2 --enable-shared > --with-pbs=/opt/torque/torque > > > > _______________________________________________ > 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] Configuration issues for mpich2-1.5b2
by Bharath Ramesh 29 Jan '13

29 Jan '13

On 1/29/2013 12:28 AM, Dave Goodell wrote: > Does the issue occur with the latest release of stock MPICH (3.0.1)? 1.5b2 was a beta release and there have been many fixes since then. I tried the latest mpich-3.0.1 and mpich2-1.5 and both give me the same error. Output from 3.0.1: ### ### Configuring hwloc core ### checking hwloc building mode... embedded configure: hwloc builddir: /home/bramesh/ARC/apps/build/mpich-3.0.1/src/pm/hydra/tools/topo/hwloc/hwloc configure: hwloc srcdir: /home/bramesh/ARC/apps/build/mpich-3.0.1/src/pm/hydra/tools/topo/hwloc/hwloc checking if want hwloc maintainer support... disabled (embedded mode) checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ checking for hwloc symbol prefix... hwloc_ checking size of void *... 0 checking which OS support to include... Linux checking which CPU support to include... unknown -- assuming x86_64 checking size of unsigned long... (cached) 8 checking size of unsigned int... 0 checking for the C compiler vendor... gnu configure line: ./configure --prefix=/home/bramesh/apps/mpich --enable-shared --with-pbs=/opt/torque/torque Output from 1.5: ### ### Configuring hwloc core ### checking hwloc building mode... embedded configure: hwloc builddir: /home/bramesh/ARC/apps/build/mpich2-1.5/src/pm/hydra/tools/topo/hwloc/hwloc configure: hwloc srcdir: /home/bramesh/ARC/apps/build/mpich2-1.5/src/pm/hydra/tools/topo/hwloc/hwloc checking if want hwloc maintainer support... disabled (embedded mode) checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ checking for hwloc symbol prefix... hwloc_ checking size of void *... 0 checking which OS support to include... Linux checking which CPU support to include... unknown -- assuming x86_64 checking size of unsigned long... (cached) 8 checking size of unsigned int... 0 checking for the C compiler vendor... gnu configure line: ./configure --prefix=/home/bramesh/apps/mpich2 --enable-shared --with-pbs=/opt/torque/torque -- Bharath

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Re: [mpich-discuss] Configuration issues for mpich2-1.5b2
by Dave Goodell 28 Jan '13

28 Jan '13

Does the issue occur with the latest release of stock MPICH (3.0.1)? 1.5b2 was a beta release and there have been many fixes since then. -Dave On Jan 28, 2013, at 9:44 PM CST, Bharath Ramesh wrote: > I hit an error while trying to build mvapich2-1.9a2 which I can reproduce with mpich2-1.5b2. When I try configuring mpich2 or mvapich2 hwloc isnt configured properly and configure ends up detecting the sizes incorrectly which results in a build failure when compiling. I reported this issue with mvapich2 mailing list[1]. > > The error I am noticing for mpich2-1.5b2 is as follows: > > ### > ### Configuring hwloc core > ### > checking hwloc building mode... embedded > configure: hwloc builddir: /home/bramesh/ARC/apps/build/mpich2-1.5b2/src/pm/hydra/tools/topo/hwloc/hwloc > configure: hwloc srcdir: /home/bramesh/ARC/apps/build/mpich2-1.5b2/src/pm/hydra/tools/topo/hwloc/hwloc > checking if want hwloc maintainer support... disabled (embedded mode) > checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ > checking for hwloc symbol prefix... hwloc_ > checking size of void *... 0 > checking which OS support to include... Linux > checking which CPU support to include... unknown -- assuming x86_64 > checking size of unsigned long... (cached) 8 > checking size of unsigned int... 0 > checking for the C compiler vendor... gnu > > configure line: > ./configure --prefix=/home/bramesh/apps/mpich2 --enable-shared --with-pbs=/opt/torque/torque > > The error I am noticing for mvapich2 is as follows: > > ### > ### Configuring hwloc core > ### > checking hwloc building mode... embedded > configure: hwloc builddir: /home/bramesh/ARC/apps/build/mvapich2-1.9a2/src/pm/hydra/tools/topo/hwloc/hwloc > configure: hwloc srcdir: /home/bramesh/ARC/apps/build/mvapich2-1.9a2/src/pm/hydra/tools/topo/hwloc/hwloc > checking if want hwloc maintainer support... disabled (embedded mode) > checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ > checking for hwloc symbol prefix... hwloc_ > checking size of void *... 0 > checking which OS support to include... Linux > checking which CPU support to include... unknown -- assuming x86_64 > checking size of unsigned long... (cached) 8 > checking size of unsigned int... 0 > checking for the C compiler vendor... gnu > > configure line: > ./configure --prefix=$HOME/apps/mvapich2 --enable-shared --with-ib-include=/opt/ofed/ofed/include --with-ib-libpath=/opt/ofed/ofed/lib64 --with-pbs=/opt/torque/torque > > If I built hwloc-1.5 or hwloc-1.6 separately in embedded mode I dont see the error. I was wondering what is the way to fix this issue so that I can build mvapich2 to use in our IB cluster. I am not subscribed to the list so would appreciate it if I am copied on the replies. > > [1] http://mail.cse.ohio-state.edu/pipermail/mvapich-discuss/2013-January/00420… > > -- > Bharath > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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