[mvapich-discuss] rpl_malloc error
Albino A. Aveleda
bino at coc.ufrj.br
Fri Oct 21 13:30:15 EDT 2011
Hi Jonathan,
Sorry for dalay. My machine was on maintenance.
I exported the variables and I compiled without problem.
Thank you for your help.
Best regards,
Bibo
----- Mensagem original -----
De: "Jonathan Perkins" <perkinjo at cse.ohio-state.edu>
Para: "Dan Kokron" <daniel.kokron at nasa.gov>
Cc: "Albino A. Aveleda" <bino at coc.ufrj.br>, mvapich-discuss at cse.ohio-state.edu
Enviadas: Quinta-feira, 20 de Outubro de 2011 15:52:24
Assunto: Re: [mvapich-discuss] rpl_malloc error
Dan, thanks for confirming this work around.
On Thu, Oct 20, 2011 at 1:43 PM, Dan Kokron <daniel.kokron at nasa.gov> wrote:
> 239 9:31 wget http://mvapich.cse.ohio-state.edu/download/mvapich2/mvapich2-1.7.tgz
> 240 9:32 tar zxf mvapich2-1.7.tgz
> 241 9:32 rm mvapich2-1.7.tgz
> 242 9:32 cd mvapich2-1.7
> 244 9:40 setenv ac_cv_func_malloc_0_nonnull yes
> 245 9:40 setenv ac_cv_func_realloc_0_nonnull yes
> 246 9:41 ./configure CC=icc CXX=icpc F77=ifort FC=ifort CFLAGS=-fpic CXXFLAGS=-fpic FFLAGS=-fpic FCFLAGS=-fpic --prefix=/u/dkokron/play/mvapich2-1.7/install/12.1.0.233 --enable-f77 --enable-fc --enable-cxx --enable-romio --with-file-system=lustre --enable-threads=default --with-device=ch3:mrail --with-rdma=gen2 --with-hwloc -disable-multi-aliases -enable-xrc=yes -enable-hybrid
> 249 10:00 gmake
> 250 10:40 gmake install
>
> The redefine of malloc is now absent from osu_benchmarks/Makefile
>
>
> On Thu, 2011-10-20 at 11:27 -0500, Jonathan Perkins wrote:
>> The osu_benchmarks are configured and compiled after the library is
>> created in the lib directory. The osu_benchmarks use -I../include and
>> -L../lib to find the necessary files of the yet to be installed
>> mvapich2 library.
>>
>> Can you try a fresh directory extracted from the tarball and then the
>> following commands?
>>
>> export ac_cv_func_malloc_0_nonnull=yes ac_cv_func_realloc_0_nonnull=yes
>> ./configure <your configure arguments>
>> make
>> make install
>>
>> The reason I'm choosing to export at the top level is because I want
>> to make sure it is in the environment when the make step is run since
>> that is when the osu benchmarks are actually configured and built.
>>
>> On Thu, Oct 20, 2011 at 11:34 AM, Dan Kokron <daniel.kokron at nasa.gov> wrote:
>> > I added the following at the top of my osu_benchmarks/configure
>> >
>> > ac_cv_func_malloc_0_nonnull=yes
>> > export ac_cv_func_malloc_0_nonnull
>> > ac_cv_func_realloc_0_nonnull=yes
>> > export ac_cv_func_realloc_0_nonnull
>> >
>> > then at the top level
>> > gmake clean
>> > configure ....
>> >
>> > malloc is still getting redefined in the osu_benchmarks/Makefile
>> >
>> > grep -n rpl_malloc osu_benchmarks/Makefile
>> > 169:DEFS = -DPACKAGE_NAME=\"OSU-Micro-Benchmarks\" -DPACKAGE_TARNAME=
>> > \"osu-micro-benchmarks\" -DPACKAGE_VERSION=\"3.4\" -DPACKAGE_STRING=
>> > \"OSU-Micro-Benchmarks\ 3.4\" -DPACKAGE_BUGREPORT=
>> > \"mvapich-discuss at cse.ohio-state.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=
>> > \"osu-micro-benchmarks\" -DVERSION=\"3.4\" -DSTDC_HEADERS=1
>> > -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
>> > -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
>> > -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
>> > -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_TIME_H=1
>> > -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=0 -Dmalloc=rpl_malloc
>> > -DHAVE_GETPAGESIZE=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_SQRT=1
>> > -DFIELD_WIDTH=20 -DFLOAT_PRECISION=2
>> >
>> > Here is some output from the config.log in the benchmark directory. Why
>> > is configure looking for -lmpich at this stage?
>> >
>> > configure:2782: checking whether the C compiler works
>> > configure:2804: ../bin/mpicc -I ../include -L ../lib -Wl,-rpath=/u/dkokron/play/mvapich2-1.7/install/12.1.0.233/lib conftest.c >&5
>> > ld: cannot find -lmpich
>> > configure:2808: $? = 1
>> > configure:2846: result: no
>> > configure: failed program was:
>> > | /* confdefs.h */
>> > | #define PACKAGE_NAME "OSU-Micro-Benchmarks"
>> > | #define PACKAGE_TARNAME "osu-micro-benchmarks"
>> > | #define PACKAGE_VERSION "3.4"
>> > | #define PACKAGE_STRING "OSU-Micro-Benchmarks 3.4"
>> > | #define PACKAGE_BUGREPORT "mvapich-discuss at cse.ohio-state.edu"
>> > | #define PACKAGE_URL ""
>> > | #define PACKAGE "osu-micro-benchmarks"
>> > | #define VERSION "3.4"
>> > | /* end confdefs.h. */
>> > |
>> > | int
>> > | main ()
>> > | {
>> > |
>> > | ;
>> > | return 0;
>> > | }
>> > configure:2851: error: in `/u/dkokron/play/mvapich2-1.7/osu_benchmarks':
>> > configure:2853: error: C compiler cannot create executables
>> >
>> > On Wed, 2011-10-19 at 17:47 -0500, Jonathan Perkins wrote:
>> >> Thanks, this is actually pretty useful. It still doesn't explain why
>> >> I've been unable to reproduce this issue in my environment but I can
>> >> at least create a patch to resolve this issue. At this point I'm
>> >> thinking about just removing AC_FUNC_MALLOC.
>> >>
>> >> Can you try the following?
>> >>
>> >> export ac_cv_func_malloc_0_nonnull=yes ac_cv_func_realloc_0_nonnull=yes
>> >> ./configure <your configure arguments>
>> >> make
>> >> make install
>> >>
>> >> This should work around the issue while I work on a more permanent
>> >> solution to this.
>> >>
>> >> On Wed, Oct 19, 2011 at 6:29 PM, Dan Kokron <daniel.kokron at nasa.gov> wrote:
>> >> > I was able to build the 1.7 release under the intel-11.0.083 compiler
>> >> > without any issues.
>> >> >
>> >> > I did a 'module purge' before loading the 12.1 environment. My env is
>> >> > pretty barren after a purge.
>> >> >
>> >> >
>> >> > I found this reference to the same issue.
>> >> > http://www.cygwin.com/ml/automake/2003-05/msg00023.html
>> >> >
>> >> > I did a search for AC_FUNC_MALLOC in all of the configure.ac under the
>> >> > 1.7 release. The only place it's present is
>> >> > osu_benchmarks/configure.ac:23:AC_FUNC_MALLOC
>> >> >
>> >> > Looking through the config.log for osu_benchmarks (see attached)
>> >> >
>> >> > grep -n rpl_malloc config.log
>> >> > 397:DEFS='-DPACKAGE_NAME=\"OSU-Micro-Benchmarks\" -DPACKAGE_TARNAME=
>> >> > \"osu-micro-benchmarks\" -DPACKAGE_VERSION=\"3.4\" -DPACKAGE_STRING=
>> >> > \"OSU-Micro-Benchmarks\ 3.4\" -DPACKAGE_BUGREPORT=
>> >> > \"mvapich-discuss at cse.ohio-state.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=
>> >> > \"osu-micro-benchmarks\" -DVERSION=\"3.4\" -DSTDC_HEADERS=1
>> >> > -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
>> >> > -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
>> >> > -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
>> >> > -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_TIME_H=1
>> >> > -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=0 -Dmalloc=rpl_malloc
>> >> > -DHAVE_GETPAGESIZE=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_SQRT=1
>> >> > -DFIELD_WIDTH=20 -DFLOAT_PRECISION=2'
>> >> > 498:#define malloc rpl_malloc
>> >> >
>> >> > hope this helps.
>> >> >
>> >> > Dan
>> >> >
>> >> > On Wed, 2011-10-19 at 16:36 -0500, Jonathan Perkins wrote:
>> >> >> Hi Dan. Does this problem occur with all versions of the intel
>> >> >> compiler or only with intel 12? I haven't been able to reproduce this
>> >> >> issue personally but I think it may be related to having both a
>> >> >> previous version of the intel compilers in my path in addition to
>> >> >> intel 12. Does this case apply to you?
>> >> >>
>> >> >> We're still looking into this but it may be helpful if you can forward
>> >> >> your config.log file from the osu_benchmarks directory as well.
>> >> >> Thanks.
>> >> >>
>> >> >> On Wed, Oct 19, 2011 at 1:50 PM, Dan Kokron <daniel.kokron at nasa.gov> wrote:
>> >> >> > I am seeing the same 'rpl_malloc' error using mvapich2-1.7
>> >> >> > (http://mvapich.cse.ohio-state.edu/download/mvapich2/mvapich2-1.7.tgz)
>> >> >> >
>> >> >> > under
>> >> >> > Intel(R) 64, Version 12.1.0.233 Build 20110811
>> >> >> >
>> >> >> > My config command is
>> >> >> > ./configure CC=icc CXX=icpc F77=ifort FC=ifort CFLAGS=-fpic
>> >> >> > CXXFLAGS=-fpic FFLAGS=-fpic FCFLAGS=-fpic
>> >> >> > --prefix=/u/dkokron/play/mvapich2-1.7/install/12.1.0.233 --enable-f77
>> >> >> > --enable-fc --enable-cxx --enable-romio --with-file-system=lustre
>> >> >> > --enable-threads=default --with-device=ch3:mrail --with-rdma=gen2
>> >> >> > --with-hwloc -disable-multi-aliases -enable-xrc=yes -enable-hybrid
>> >> >> >
>> >> >> >
>> >> >> > ../bin/mpicc -DPACKAGE_NAME=\"OSU-Micro-Benchmarks\" -DPACKAGE_TARNAME=
>> >> >> > \"osu-micro-benchmarks\" -DPACKAGE_VERSION=\"3.4\" -DPACKAGE_STRING=
>> >> >> > \"OSU-Micro-Benchmarks\ 3.4\" -DPACKAGE_BUGREPORT=
>> >> >> > \"mvapich-discuss at cse.ohio-state.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=
>> >> >> > \"osu-micro-benchmarks\" -DVERSION=\"3.4\" -DSTDC_HEADERS=1
>> >> >> > -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
>> >> >> > -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
>> >> >> > -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
>> >> >> > -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_TIME_H=1
>> >> >> > -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=0 -Dmalloc=rpl_malloc
>> >> >> > -DHAVE_GETPAGESIZE=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_SQRT=1
>> >> >> > -DFIELD_WIDTH=20 -DFLOAT_PRECISION=2 -I. -I ../include -g -O2 -c
>> >> >> > osu_alltoall.c
>> >> >> > ../bin/mpicc -g -O2 -L ../lib
>> >> >> > -Wl,-rpath=/u/dkokron/play/mvapich2-1.7/install/12.1.0.233/lib -o
>> >> >> > osu_alltoall osu_alltoall.o
>> >> >> > osu_alltoall.o: In function `main':
>> >> >> > /home1/dkokron/play/mvapich2-1.7/osu_benchmarks/osu_alltoall.c:82:
>> >> >> > undefined reference to `rpl_malloc'
>> >> >> > /home1/dkokron/play/mvapich2-1.7/osu_benchmarks/osu_alltoall.c:91:
>> >> >> > undefined reference to `rpl_malloc'
>> >> >> >
>> >> >> > Just to be sure.
>> >> >> >
>> >> >> > bin/mpicc -V
>> >> >> > Intel(R) C Intel(R) 64 Compiler XE for applications running on Intel(R)
>> >> >> > 64, Version 12.1.0.233 Build 20110811
>> >> >> > Copyright (C) 1985-2011 Intel Corporation. All rights reserved.
>> >> >> >
>> >> >> >
>> >> >> > On Fri, 2011-10-14 at 14:10 -0500, Jonathan Perkins wrote:
>> >> >> >> It looks like you may be hitting a different error for 1.7rc2 compared
>> >> >> >> to 1.6. Can you send me the config.log from both the top level
>> >> >> >> directory and the osu_benchmarks sub directory.
>> >> >> >>
>> >> >> >> Also can you provide the exact steps needed to reproduce this? I've
>> >> >> >> quickly tried both 1.6 and 1.7rc2 with the intel12 compilers and I was
>> >> >> >> unable to see this problem.
>> >> >> >>
>> >> >> >> On Fri, Oct 14, 2011 at 1:05 PM, Albino A. Aveleda <bino at coc.ufrj.br> wrote:
>> >> >> >> > Hi All,
>> >> >> >> >
>> >> >> >> > I am using SLES11SP1 and below you have more details about the error.
>> >> >> >> >
>> >> >> >> > Intel(R) C Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 12.1.0.233 Build 20110811
>> >> >> >> > Copyright (C) 1985-2011 Intel Corporation. All rights reserved.
>> >> >> >> > configure:2761: $? = 0
>> >> >> >> > configure:2750: ../bin/mpicc -qversion >&5
>> >> >> >> > icc: command line warning #10006: ignoring unknown option '-qversion'
>> >> >> >> > /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crt1.o: In function `_start':
>> >> >> >> > /usr/src/packages/BUILD/glibc-2.11.1/csu/../sysdeps/x86_64/elf/start.S:109: undefined reference to `main'
>> >> >> >> > configure:2761: $? = 1
>> >> >> >> > configure:2781: checking whether the C compiler works
>> >> >> >> > configure:2803: ../bin/mpicc -I ../include -L ../lib -Wl,-rpath=/sw/mpi/mvapich2/1.7rc2-intel/lib conftest.c >&5
>> >> >> >> > configure:2807: $? = 0
>> >> >> >> > configure:2855: result: yes
>> >> >> >> > configure:2858: checking for C compiler default output file name
>> >> >> >> > configure:2860: result: a.out
>> >> >> >> > configure:2866: checking for suffix of executables
>> >> >> >> > configure:2873: ../bin/mpicc -o conftest -I ../include -L ../lib -Wl,-rpath=/sw/mpi/mvapich2/1.7rc2-intel/lib conftest.c >&5
>> >> >> >> > configure:2877: $? = 0
>> >> >> >> > configure:2899: result:
>> >> >> >> > configure:2921: checking whether we are cross compiling
>> >> >> >> > configure:2929: ../bin/mpicc -o conftest -I ../include -L ../lib -Wl,-rpath=/sw/mpi/mvapich2/1.7rc2-intel/lib conftest.c >&5
>> >> >> >> > configure:2933: $? = 0
>> >> >> >> > configure:2940: ./conftest
>> >> >> >> > /sw/src/mvapich2/mvapich2-1.7rc2/osu_benchmarks/configure: line 2942: 31101 Segmentation fault ./conftest$ac_cv_exeext
>> >> >> >> > configure:2944: $? = 139
>> >> >> >> > configure:2951: error: in `/sw/src/mvapich2/mvapich2-1.7rc2/osu_benchmarks':
>> >> >> >> > configure:2953: error: cannot run C compiled programs.
>> >> >> >> >
>> >> >> >> > Regards,
>> >> >> >> >
>> >> >> >> > ----- Original Message -----
>> >> >> >> > From: "Albino A. Aveleda" <bino at coc.ufrj.br>
>> >> >> >> > To: mvapich-discuss at cse.ohio-state.edu
>> >> >> >> > Sent: Friday, October 14, 2011 9:30:18 AM
>> >> >> >> > Subject: [mvapich-discuss] rpl_malloc error
>> >> >> >> >
>> >> >> >> > Hi All,
>> >> >> >> >
>> >> >> >> > I compiled the mvapich2-1.6 with gcc witout problem, but
>> >> >> >> > when I try to compile with intel compiler version 12 I
>> >> >> >> > receive this error.
>> >> >> >> >
>> >> >> >> > make[2]: Entering directory `/sw/src/mvapich2/mvapich2-1.6/osu_benchmarks'
>> >> >> >> > ../bin/mpicc -g -O2 -L ../lib -Wl,-rpath=/sw/mpi/mvapich2/1.6-intel/lib -o osu_alltoall osu_alltoall.o
>> >> >> >> > osu_alltoall.o: In function `main':
>> >> >> >> > /sw/src/mvapich2/mvapich2-1.6/osu_benchmarks/osu_alltoall.c:69: undefined reference to `rpl_malloc'
>> >> >> >> > /sw/src/mvapich2/mvapich2-1.6/osu_benchmarks/osu_alltoall.c:78: undefined reference to `rpl_malloc'
>> >> >> >> > make[2]: *** [osu_alltoall] Error 1
>> >> >> >> > make[2]: Leaving directory `/sw/src/mvapich2/mvapich2-1.6/osu_benchmarks'
>> >> >> >> > make[1]: *** [all-postamble] Error 2
>> >> >> >> > make[1]: Leaving directory `/sw/src/mvapich2/mvapich2-1.6'
>> >> >> >> > make: *** [all-redirect] Error 2
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > How do I fix this?
>> >> >> >> >
>> >> >> >> > Regards,
>> >> >> >> > Bibo
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