[mvapich-discuss] rpl_malloc error
Dan Kokron
daniel.kokron at nasa.gov
Thu Oct 20 11:34:11 EDT 2011
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
> >> >> > _______________________________________________
> >> >> > 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
> >
>
>
>
--
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
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