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

Re: [mpich-discuss] libintlc.so.5 not found while configuring
by Seungbum Koo 05 Sep '13

05 Sep '13

Thank you for your advice. But nothing has changed even if I add that line at the stage of configure. So this is what I wrote in the command line. ======================================================================== sudo /opt/mpich/mpich-3.0.4-source/configure --prefix=/opt/mpich/ CC=/opt/intel/composer_xe_2013_sp1.0.080/bin/intel64/icc CXX=/opt/intel/composer_xe_2013_sp1.0.080/bin/intel64/icpc F77=/opt/intel/composer_xe_2013_sp1.0.080/bin/intel64/ifort FC=/opt/intel/composer_xe_2013_sp1.0.080/bin/intel64/ifort LDFLAGS="-L/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64" --enable-fast=all,O3 --enable-g=dbg,mem,log --enable-shared --with-pm=hydra 2>&1 | sudo tee log_configure.txt ================================================================ What 'configure' says: ====================================================== ld: warning: libintlc.so.5, needed by /opt/intel/composer_xe_2013_ sp1.0.080/compiler/lib/intel64/libifport.so.5, not found (try using -rpath or -rpath-link) ====================================================== What 'make' says: ================================================================ ld: warning: libimf.so, needed by /opt/mpich/mpich-3.0.4-build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath-link) ld: warning: libsvml.so, needed by /opt/mpich/mpich-3.0.4-build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath-link) ld: warning: libirng.so, needed by /opt/mpich/mpich-3.0.4-build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath-link) ld: warning: libintlc.so.5, needed by /opt/mpich/mpich-3.0.4-build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath-link) ================================================================ Not a single line difference as before. Does it make sense? "libifport.so.5" needs "libintlc.so.5" but they are in the same directory. And those 'not found' files at the 'make' stage as well. They are all in '/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/ intel64/'. Any idea? Seungbum

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Re: [mpich-discuss] libintlc.so.5 not found while configuring
by Antonio J. Peña 05 Sep '13

05 Sep '13

You can try with: LDFLAGS="-L */opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64"* in your configure line (or wherever libintlc.so.5 is). LD_LIBRARY_PATH is to find them at runtime, while LDFLAGS does it at compile time. Antonio On Thursday, September 05, 2013 05:33:12 PM Seungbum Koo wrote: I hope this to be the last question. While configuring, I see a warning message as follows from "config.log". =============================================== =======ld: warning: libintlc.so.5, needed by /opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64/libifport.so.5, not found (try using -rpath or -rpath- link)============================================ ========== I googled a bit and found out that this is about an intel library issue. And it says about $LD_LIBRARY_PATH and so on. Well, but my $LD_LIBRARY_PATH has the directory where "libintlc.so.5" is. =============================================== =======simba@asterix:/opt/mpich/mpich-3.0.4-build$ echo $LD_LIBRARY_PATH */opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64*:/opt/intel/co mposer_xe_2013_sp1.0.080/mpirt/lib/intel64:/opt/intel/composer_xe_2013_s p1.0.080/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/ ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64:/ opt/intel/composer_xe_2013_sp1.0.080/mkl/lib/intel64:/opt/intel/composer_ xe_2013_sp1.0.080/tbb/lib/intel64/gcc4.4simba@asterix:/opt/mpich/mpich-3 .0.4- build$=========================================== =========== If I go on to "make", then it shows following warnings from the screen. =============================================== =======ld: warning: libimf.so, needed by /opt/mpich/mpich-3.0.4- build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath-link)ld: warning: libsvml.so, needed by /opt/mpich/mpich-3.0.4- build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath-link)ld: warning: libirng.so, needed by /opt/mpich/mpich-3.0.4- build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath-link)ld: warning: libintlc.so.5, needed by /opt/mpich/mpich-3.0.4- build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath- link)============================================ ========== If I keep proceed and install MPICH, "mpiexec" seems to work. I tested with "cpi" in example. The problem is, when I try to install PETSc, it complains about the same issue (missing those *.so(.5) files) and don't configure any more. I tried "--download-mpich=1" option from PETSc without installing MPICH separately, but the result was the same. It keeps complaining those missing(?) files, which are actually in */opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64* directory. Does anyone has an idea what else can I do? Seungbum -- Antonio J. Peña Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240, Of. 3148 Argonne, IL 60439-4847 (+1) 630-252-7928 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya

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libintlc.so.5 not found while configuring
by Seungbum Koo 05 Sep '13

05 Sep '13

I hope this to be the last question. While configuring, I see a warning message as follows from "config.log". ====================================================== ld: warning: libintlc.so.5, needed by /opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64/libifport.so.5, not found (try using -rpath or -rpath-link) ====================================================== I googled a bit and found out that this is about an intel library issue. And it says about $LD_LIBRARY_PATH and so on. Well, but my $LD_LIBRARY_PATH has the directory where "libintlc.so.5" is. ====================================================== simba@asterix:/opt/mpich/mpich-3.0.4-build$ echo $LD_LIBRARY_PATH */opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64* :/opt/intel/composer_xe_2013_sp1.0.080/mpirt/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/tbb/lib/intel64/gcc4.4 simba@asterix:/opt/mpich/mpich-3.0.4-build$ ====================================================== If I go on to "make", then it shows following warnings from the screen. ====================================================== ld: warning: libimf.so, needed by /opt/mpich/mpich-3.0.4-build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath-link) ld: warning: libsvml.so, needed by /opt/mpich/mpich-3.0.4-build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath-link) ld: warning: libirng.so, needed by /opt/mpich/mpich-3.0.4-build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath-link) ld: warning: libintlc.so.5, needed by /opt/mpich/mpich-3.0.4-build/src/mpl/.libs/libmpl.so, not found (try using -rpath or -rpath-link) ====================================================== If I keep proceed and install MPICH, "mpiexec" seems to work. I tested with "cpi" in example. The problem is, when I try to install PETSc, it complains about the same issue (missing those *.so(.5) files) and don't configure any more. I tried "--download-mpich=1" option from PETSc without installing MPICH separately, but the result was the same. It keeps complaining those missing(?) files, which are actually in * /opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64* directory. Does anyone has an idea what else can I do? Seungbum

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Re: [mpich-discuss] trouble in 'make' stage
by Seungbum Koo 05 Sep '13

05 Sep '13

I looks like some other conversation is going on. I hate when this kind of thing happens, but I erased mpich and intel compiler and started over again from installing intel compiler, that EOF error didn't occur at this time. Sorry. Anyway, libtool I have here was ==================================================================== simba@asterix:/opt/mpich/mpich-3.0.4-build$ ./libtool --version libtool (GNU libtool) 2.4.2 Written by Gordon Matzigkeit <gord(a)gnu.ai.mit.edu>, 1996 Copyright (C) 2011 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. simba@asterix:/opt/mpich/mpich-3.0.4-build$ ==================================================================== and libtool itself is attached. On Thu, Sep 5, 2013 at 4:48 PM, Antonio J. Peña <apenya(a)mcs.anl.gov> wrote: > > Well, your log_make.txt says that the libtool script finds a problem in > lines > 6444-6445. So yes, you have it, and yes, MPICH uses it for compilation. It > is > generated by configure. > > On the other hand, autogen.sh is not needed for end users, so you can skip > what I said about it if you didn't run it. > > Antonio > > > On Thursday, September 05, 2013 11:25:47 PM Reuti wrote: > > Hi, > > > > Am 05.09.2013 um 23:03 schrieb Antonio J. Peña: > > > Which version of libtool are you using? (libtool --version) > > > > > > Please attach your libtool script located in the root building > directory > > > so that we can check what's going on on lines 6444-6445. > > > > > > Also, the output of autogen.sh might be useful here. > > > > Are these two tools necessary to compile MPICH? I can compile it without > > having them installed at all. > > > > -- Reuti > > > > > Antonio > > > > > > On Thursday, September 05, 2013 02:23:12 PM Seungbum Koo wrote: > > > Hello everyone. > > > > > > I have trouble with 'make' at this time. > > > > > > Now it says it encountered an unexpected EOF when dealing with > libmpl.la. > > > log files for 'configure' and 'make' stages are attached. > > > > > > Any help will be appreciated. > > > > > > Seungbum > > > _______________________________________________ > > > 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 > -- > Antonio J. Peña > Postdoctoral Appointee > Mathematics and Computer Science Division > Argonne National Laboratory > 9700 South Cass Avenue, Bldg. 240, Of. 3148 > Argonne, IL 60439-4847 > (+1) 630-252-7928 > apenya(a)mcs.anl.gov > www.mcs.anl.gov/~apenya > _______________________________________________ > 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] trouble in 'make' stage
by Antonio J. Peña 05 Sep '13

05 Sep '13

Well, your log_make.txt says that the libtool script finds a problem in lines 6444-6445. So yes, you have it, and yes, MPICH uses it for compilation. It is generated by configure. On the other hand, autogen.sh is not needed for end users, so you can skip what I said about it if you didn't run it. Antonio On Thursday, September 05, 2013 11:25:47 PM Reuti wrote: > Hi, > > Am 05.09.2013 um 23:03 schrieb Antonio J. Peña: > > Which version of libtool are you using? (libtool --version) > > > > Please attach your libtool script located in the root building directory > > so that we can check what's going on on lines 6444-6445. > > > > Also, the output of autogen.sh might be useful here. > > Are these two tools necessary to compile MPICH? I can compile it without > having them installed at all. > > -- Reuti > > > Antonio > > > > On Thursday, September 05, 2013 02:23:12 PM Seungbum Koo wrote: > > Hello everyone. > > > > I have trouble with 'make' at this time. > > > > Now it says it encountered an unexpected EOF when dealing with libmpl.la. > > log files for 'configure' and 'make' stages are attached. > > > > Any help will be appreciated. > > > > Seungbum > > _______________________________________________ > > 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 -- Antonio J. Peña Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240, Of. 3148 Argonne, IL 60439-4847 (+1) 630-252-7928 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya

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Re: [mpich-discuss] trouble in 'make' stage
by Reuti 05 Sep '13

05 Sep '13

Hi, Am 05.09.2013 um 21:23 schrieb Seungbum Koo: > I have trouble with 'make' at this time. > > Now it says it encountered an unexpected EOF when dealing with libmpl.la. log files for 'configure' and 'make' stages are attached. > > Any help will be appreciated. Did you clean up your build directory after your initial attempt? -- Reuti

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Re: [mpich-discuss] trouble in 'make' stage
by Reuti 05 Sep '13

05 Sep '13

Hi, Am 05.09.2013 um 23:03 schrieb Antonio J. Peña: > Which version of libtool are you using? (libtool --version) > > Please attach your libtool script located in the root building directory so that we can check what's going on on lines 6444-6445. > > Also, the output of autogen.sh might be useful here. Are these two tools necessary to compile MPICH? I can compile it without having them installed at all. -- Reuti > Antonio > > > On Thursday, September 05, 2013 02:23:12 PM Seungbum Koo wrote: > Hello everyone. > > I have trouble with 'make' at this time. > > Now it says it encountered an unexpected EOF when dealing with libmpl.la. log files for 'configure' and 'make' stages are attached. > > Any help will be appreciated. > > Seungbum > _______________________________________________ > 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] trouble in 'make' stage
by Antonio J. Peña 05 Sep '13

05 Sep '13

Hi, Which version of libtool are you using? (libtool --version) Please attach your libtool script located in the root building directory so that we can check what's going on on lines 6444-6445. Also, the output of autogen.sh might be useful here. Antonio On Thursday, September 05, 2013 02:23:12 PM Seungbum Koo wrote: Hello everyone. I have trouble with 'make' at this time. Now it says it encountered an unexpected EOF when dealing with libmpl.la[1]. log files for 'configure' and 'make' stages are attached. Any help will be appreciated. Seungbum -------- [1] http://libmpl.la

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Re: [mpich-discuss] compilation error
by Ken Raffenetti 05 Sep '13

05 Sep '13

Can you send us the config.log in src/pm/hydra? ----- Original Message ----- > From: "Suraj Prabhakaran" <suraj.prabhakaran(a)gmail.com> > To: discuss(a)mpich.org > Sent: Thursday, September 5, 2013 2:38:18 PM > Subject: [mpich-discuss] compilation error > > Hello, > > When I try to compile mpich in my system, I get the following error. > Can someone hint about this? > > Best, > Suraj > > Making all in tools/topo/hwloc/hwloc > make[3]: Entering directory > `/root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc' > Making all in src > make[4]: Entering directory > `/root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc/src' > make[5]: Entering directory > `/root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc/src' > CC topology.lo > CC traversal.lo > CC distances.lo > CC components.lo > CC bind.lo > CC bitmap.lo > CC misc.lo > CC base64.lo > /root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h(41): > catastrophic error: #error directive: "unknown size for unsigned > int." > #error "unknown size for unsigned int." > ^ > > /root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h(41): > catastrophic error: #error directive: "unknown size for unsigned > int." > #error "unknown size for unsigned int." > ^ > > /root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h(41): > catastrophic error: #error directive: "unknown size for unsigned > int." > #error "unknown size for unsigned int." > ^ > > compilation aborted for traversal.c (code 4) > compilation aborted for bitmap.c (code 4) > compilation aborted for misc.c (code 4) > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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compilation error
by Suraj Prabhakaran 05 Sep '13

05 Sep '13

Hello, When I try to compile mpich in my system, I get the following error. Can someone hint about this? Best, Suraj Making all in tools/topo/hwloc/hwloc make[3]: Entering directory `/root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc' Making all in src make[4]: Entering directory `/root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc/src' make[5]: Entering directory `/root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc/src' CC topology.lo CC traversal.lo CC distances.lo CC components.lo CC bind.lo CC bitmap.lo CC misc.lo CC base64.lo /root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h(41): catastrophic error: #error directive: "unknown size for unsigned int." #error "unknown size for unsigned int." ^ /root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h(41): catastrophic error: #error directive: "unknown size for unsigned int." #error "unknown size for unsigned int." ^ /root/mpi/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h(41): catastrophic error: #error directive: "unknown size for unsigned int." #error "unknown size for unsigned int." ^ compilation aborted for traversal.c (code 4) compilation aborted for bitmap.c (code 4) compilation aborted for misc.c (code 4)

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