[mvapich-discuss] rpl_malloc error

Wed Oct 19 18:47:34 EDT 2011

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
>> >> > _______________________________________________
>> >> > mvapich-discuss mailing list
>> >> > mvapich-discuss at cse.ohio-state.edu
>> >> > http://mail.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
>> >> >
>> >> > --
>> >> >
>> >> > __________________________________________________
>> >> > Albino A. Aveleda                 bino at coc.ufrj.br
>> >> > System Engineer                   +55 21 2562-8080
>> >> > PEC-COPPE/UFRJ                    +55 21 2562-8465
>> >> > Federal University of Rio de Janeiro (UFRJ)
>> >> > _______________________________________________
>> >> > mvapich-discuss mailing list
>> >> > mvapich-discuss at cse.ohio-state.edu
>> >> > http://mail.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Jonathan Perkins
>> >> http://www.cse.ohio-state.edu/~perkinjo
>> >>
>> >> _______________________________________________
>> >> mvapich-discuss mailing list
>> >> mvapich-discuss at cse.ohio-state.edu
>> >> http://mail.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
>> > --
>> > Dan Kokron
>> > Global Modeling and Assimilation Office, Code 610.1
>> > NASA Goddard Space Flight Center
>> > Greenbelt, MD 20771 USA
>> > Daniel.S.Kokron at nasa.gov
>> > Phone: (301) 614-5192
>> > Fax:   (301) 614-5304
>> >
>> >
>>
>>
>>
> --
> Dan Kokron
> Global Modeling and Assimilation Office, Code 610.1
> NASA Goddard Space Flight Center
> Greenbelt, MD 20771 USA
> Daniel.S.Kokron at nasa.gov
> Phone: (301) 614-5192
> Fax:   (301) 614-5304
>

-- 
Jonathan Perkins
http://www.cse.ohio-state.edu/~perkinjo