[OMPI users] Segmentation Fault (Core Dumped) on mpif90 -v

Discussion:

Giacomo Rossi

2016-05-05 06:50:55 UTC

Iâve installed the latest version of Intel Parallel Studio (16.0.3), then
Iâve downloaded the latest version of openmpi (1.10.2) and Iâve compiled it
with

`./configure CC=icc CXX=icpc F77=ifort FC=ifort
--prefix=/opt/openmpi/1.10.2/intel/16.0.3`

then I've installed and everything seems ok, but when I try the simple
command

' /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v'

I receive the following error

'Segmentation fault (core dumped)'

I'm on ArchLinux, with kernel 4.5.1-1-ARCH; I've attache to this email the
config.log file compressed with bzip2.

Any help will be appreciated!

Giacomo Rossi Ph.D., Space Engineer

Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
*p: *(+39) 0692927207 | *m**: *(+39) 3408816643 | *e: ****@gmail.com
<***@uniroma1.it>
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>

â

Gilles Gouaillardet

2016-05-05 07:37:45 UTC

Permalink

Giacomo,

could you also open the core file with gdb and post the backtrace ?

can you also
ldd mpif90
and confirm no intel MPI library is used ?

btw, the OpenMPI fortran wrapper is now mpifort

Cheers,

Gilles

Post by Giacomo Rossi
Iâve installed the latest version of Intel Parallel Studio (16.0.3), then
Iâve downloaded the latest version of openmpi (1.10.2) and Iâve compiled it
with
`./configure CC=icc CXX=icpc F77=ifort FC=ifort
--prefix=/opt/openmpi/1.10.2/intel/16.0.3`
then I've installed and everything seems ok, but when I try the simple
command
' /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v'
I receive the following error
'Segmentation fault (core dumped)'
I'm on ArchLinux, with kernel 4.5.1-1-ARCH; I've attache to this email the
config.log file compressed with bzip2.
Any help will be appreciated!
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>
â

Giacomo Rossi

2016-05-05 08:44:22 UTC

Permalink

Here the result of ldd command:
'ldd /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
linux-vdso.so.1 (0x00007ffcacbbe000)
libopen-pal.so.13 => /opt/openmpi/1.10.2/intel/16.0.3/lib/libopen-pal.so.13
(0x00007fa9597a9000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007fa9594a4000)
libpciaccess.so.0 => /usr/lib/libpciaccess.so.0 (0x00007fa95929a000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fa959096000)
librt.so.1 => /usr/lib/librt.so.1 (0x00007fa958e8e000)
libutil.so.1 => /usr/lib/libutil.so.1 (0x00007fa958c8b000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fa958a75000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fa958858000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007fa9584b7000)
libimf.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libimf.so
(0x00007fa957fb9000)
libsvml.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libsvml.so
(0x00007fa9570ad000)
libirng.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libirng.so
(0x00007fa956d3b000)
libintlc.so.5 =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libintlc.so.5
(0x00007fa956acf000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa959ab9000)'

I can't provide a core file, because I can't compile or launch any program
with mpifort... I've always the error 'core dumped' also when I try to
compile a program with mpifort, and of course there isn't any core file.

Giacomo Rossi Ph.D., Space Engineer

Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
*p: *(+39) 0692927207 | *m**: *(+39) 3408816643 | *e: ****@gmail.com
<***@uniroma1.it>
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>

Gilles Gouaillardet

2016-05-05 09:11:04 UTC

Permalink

Giacomo,

one option is to (if your shell is bash)
ulimit -c unlimited
mpif90 -v
you should get a core file

an other option is to
gdb /.../mpif90
r -v
bt

Cheers,

Gilles

Post by Giacomo Rossi
'ldd /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
linux-vdso.so.1 (0x00007ffcacbbe000)
libopen-pal.so.13 =>
/opt/openmpi/1.10.2/intel/16.0.3/lib/libopen-pal.so.13 (0x00007fa9597a9000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007fa9594a4000)
libpciaccess.so.0 => /usr/lib/libpciaccess.so.0 (0x00007fa95929a000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fa959096000)
librt.so.1 => /usr/lib/librt.so.1 (0x00007fa958e8e000)
libutil.so.1 => /usr/lib/libutil.so.1 (0x00007fa958c8b000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fa958a75000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fa958858000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007fa9584b7000)
libimf.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libimf.so
(0x00007fa957fb9000)
libsvml.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libsvml.so
(0x00007fa9570ad000)
libirng.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libirng.so
(0x00007fa956d3b000)
libintlc.so.5 =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libintlc.so.5
(0x00007fa956acf000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa959ab9000)'
I can't provide a core file, because I can't compile or launch any program
with mpifort... I've always the error 'core dumped' also when I try to
compile a program with mpifort, and of course there isn't any core file.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>

Post by Giacomo Rossi
Iâve installed the latest version of Intel Parallel Studio (16.0.3), then
Iâve downloaded the latest version of openmpi (1.10.2) and Iâve compiled it
with
`./configure CC=icc CXX=icpc F77=ifort FC=ifort
--prefix=/opt/openmpi/1.10.2/intel/16.0.3`
then I've installed and everything seems ok, but when I try the simple
command
' /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v'
I receive the following error
'Segmentation fault (core dumped)'
I'm on ArchLinux, with kernel 4.5.1-1-ARCH; I've attache to this email
the config.log file compressed with bzip2.
Any help will be appreciated!
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
*p: *(+39) 0692927207 | *m**: *(+39) 3408816643 | *e: *
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>
â

Giacomo Rossi

2016-05-05 09:15:10 UTC

Permalink

gdb /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
GNU gdb (GDB) 7.11
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-pc-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90...(no
debugging symbols found)...done.
(gdb) r -v
Starting program: /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff6858f38 in ?? ()
(gdb) bt
#0 0x00007ffff6858f38 in ?? ()
#1 0x00007ffff7de5828 in _dl_relocate_object () from
/lib64/ld-linux-x86-64.so.2
#2 0x00007ffff7ddcfa3 in dl_main () from /lib64/ld-linux-x86-64.so.2
#3 0x00007ffff7df029c in _dl_sysdep_start () from
/lib64/ld-linux-x86-64.so.2
#4 0x00007ffff7dddd4a in _dl_start () from /lib64/ld-linux-x86-64.so.2
#5 0x00007ffff7dd9d98 in _start () from /lib64/ld-linux-x86-64.so.2
#6 0x0000000000000002 in ?? ()
#7 0x00007fffffffaa8a in ?? ()
#8 0x00007fffffffaab6 in ?? ()
#9 0x0000000000000000 in ?? ()

Giacomo Rossi Ph.D., Space Engineer

Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
*p: *(+39) 0692927207 | *m**: *(+39) 3408816643 | *e: ****@gmail.com
<***@uniroma1.it>
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>

Post by Giacomo Rossi
Iâve installed the latest version of Intel Parallel Studio (16.0.3), then
Iâve downloaded the latest version of openmpi (1.10.2) and Iâve compiled it
with
`./configure CC=icc CXX=icpc F77=ifort FC=ifort
--prefix=/opt/openmpi/1.10.2/intel/16.0.3`
then I've installed and everything seems ok, but when I try the simple
command
' /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v'
I receive the following error
'Segmentation fault (core dumped)'
I'm on ArchLinux, with kernel 4.5.1-1-ARCH; I've attache to this email
the config.log file compressed with bzip2.
Any help will be appreciated!
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
*p: *(+39) 0692927207 | *m**: *(+39) 3408816643 | *e: *
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>
â

Gus Correa

2016-05-05 16:02:47 UTC

Permalink

Hi Giacomo

Some programs fail with segmentation fault
because the stack size is too small.
[But others because of bugs in memory allocation/management, etc.]

Have you tried

ulimit -s unlimited

before you run the program?

Are you using a single machine or a cluster?
If you're using infiniband you may need also to make the locked memory
unlimited:

ulimit -l unlimited

I hope this helps,
Gus Correa

Post by Giacomo Rossi
gdb /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
GNU gdb (GDB) 7.11
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
<http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-pc-linux-gnu".
Type "show configuration" for configuration details.
<http://www.gnu.org/software/gdb/bugs/>.
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90...(no
debugging symbols found)...done.
(gdb) r -v
Starting program: /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff6858f38 in ?? ()
(gdb) bt
#0 0x00007ffff6858f38 in ?? ()
#1 0x00007ffff7de5828 in _dl_relocate_object () from
/lib64/ld-linux-x86-64.so.2
#2 0x00007ffff7ddcfa3 in dl_main () from /lib64/ld-linux-x86-64.so.2
#3 0x00007ffff7df029c in _dl_sysdep_start () from
/lib64/ld-linux-x86-64.so.2
#4 0x00007ffff7dddd4a in _dl_start () from /lib64/ld-linux-x86-64.so.2
#5 0x00007ffff7dd9d98 in _start () from /lib64/ld-linux-x86-64.so.2
#6 0x0000000000000002 in ?? ()
#7 0x00007fffffffaa8a in ?? ()
#8 0x00007fffffffaab6 in ?? ()
#9 0x0000000000000000 in ?? ()
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering,
"Sapienza" University of Rome
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>
'ldd /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
linux-vdso.so.1 (0x00007ffcacbbe000)
libopen-pal.so.13 =>
/opt/openmpi/1.10.2/intel/16.0.3/lib/libopen-pal.so.13
(0x00007fa9597a9000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007fa9594a4000)
libpciaccess.so.0 => /usr/lib/libpciaccess.so.0 (0x00007fa95929a000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fa959096000)
librt.so.1 => /usr/lib/librt.so.1 (0x00007fa958e8e000)
libutil.so.1 => /usr/lib/libutil.so.1 (0x00007fa958c8b000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fa958a75000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fa958858000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007fa9584b7000)
libimf.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libimf.so
(0x00007fa957fb9000)
libsvml.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libsvml.so
(0x00007fa9570ad000)
libirng.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libirng.so
(0x00007fa956d3b000)
libintlc.so.5 =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libintlc.so.5
(0x00007fa956acf000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa959ab9000)'
I can't provide a core file, because I can't compile or launch any
program with mpifort... I've always the error 'core dumped' also
when I try to compile a program with mpifort, and of course there
isn't any core file.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace
Engineering, "Sapienza" University of Rome
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>
I’ve installed the latest version of Intel Parallel Studio
(16.0.3), then I’ve downloaded the latest version of openmpi
(1.10.2) and I’ve compiled it with
`./configure CC=icc CXX=icpc F77=ifort FC=ifort
--prefix=/opt/openmpi/1.10.2/intel/16.0.3`
then I've installed and everything seems ok, but when I try the
simple command
' /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v'
I receive the following error
'Segmentation fault (core dumped)'
I'm on ArchLinux, with kernel 4.5.1-1-ARCH; I've attache to this
email the config.log file compressed with bzip2.
Any help will be appreciated!
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace
Engineering, "Sapienza" University of Rome
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>

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Jeff Squyres (jsquyres)

2016-05-05 16:04:33 UTC

Permalink

Giacomo --

Are you able to run anything that is compiled by that Intel compiler installation?

Post by Gus Correa
Hi Giacomo
Some programs fail with segmentation fault
because the stack size is too small.
[But others because of bugs in memory allocation/management, etc.]
Have you tried
ulimit -s unlimited
before you run the program?
Are you using a single machine or a cluster?
ulimit -l unlimited
I hope this helps,
Gus Correa

_______________________________________________
users mailing list
Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users
Link to this post: http://www.open-mpi.org/community/lists/users/2016/05/29098.php

--
Jeff Squyres
***@cisco.com
For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/

Dave Love

2016-05-06 12:27:45 UTC

Permalink

Post by Gus Correa
Hi Giacomo
Some programs fail with segmentation fault
because the stack size is too small.

Yes, the default for Intel Fortran is to allocate large-ish amounts on
the stack, which may matter when the compiled program runs.

However, look at the backtrace. It's apparently coming from the loader,
so something is pretty screwed up, though I can't guess what. It would
help to have debugging symbols; always use at least -g and have
GNU/Linux distribution debuginfo packages to hand.

[Probably not relevant in this case, but I try to solve problems with
the Intel compiler and MPI (sorry Jeff et al) by persuading users to
avoid them. GCC is more reliable in my experience, and the story about
its supposedly poor code generation isn't supported by experiment (if
that counts for anything these days).]

Post by Gus Correa
[But others because of bugs in memory allocation/management, etc.]
Have you tried
ulimit -s unlimited
before you run the program?
Are you using a single machine or a cluster?
If you're using infiniband you may need also to make the locked memory
ulimit -l unlimited
I hope this helps,
Gus Correa

Giacomo Rossi

2016-05-06 07:45:15 UTC

Permalink

Post by Giacomo Rossi
'ldd /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
linux-vdso.so.1 (0x00007ffcacbbe000)
libopen-pal.so.13 =>
/opt/openmpi/1.10.2/intel/16.0.3/lib/libopen-pal.so.13 (0x00007fa9597a9000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007fa9594a4000)
libpciaccess.so.0 => /usr/lib/libpciaccess.so.0 (0x00007fa95929a000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fa959096000)
librt.so.1 => /usr/lib/librt.so.1 (0x00007fa958e8e000)
libutil.so.1 => /usr/lib/libutil.so.1 (0x00007fa958c8b000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fa958a75000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fa958858000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007fa9584b7000)
libimf.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libimf.so
(0x00007fa957fb9000)
libsvml.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libsvml.so
(0x00007fa9570ad000)
libirng.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libirng.so
(0x00007fa956d3b000)
libintlc.so.5 =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libintlc.so.5
(0x00007fa956acf000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa959ab9000)'
I can't provide a core file, because I can't compile or launch any
program with mpifort... I've always the error 'core dumped' also when I try
to compile a program with mpifort, and of course there isn't any core file.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
*p: *(+39) 0692927207 | *m**: *(+39) 3408816643 | *e: *
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>

Post by Giacomo Rossi
Iâve installed the latest version of Intel Parallel Studio (16.0.3),
then Iâve downloaded the latest version of openmpi (1.10.2) and Iâve
compiled it with
`./configure CC=icc CXX=icpc F77=ifort FC=ifort
--prefix=/opt/openmpi/1.10.2/intel/16.0.3`
then I've installed and everything seems ok, but when I try the simple
command
' /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v'
I receive the following error
'Segmentation fault (core dumped)'
I'm on ArchLinux, with kernel 4.5.1-1-ARCH; I've attache to this email
the config.log file compressed with bzip2.
Any help will be appreciated!
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
*p: *(+39) 0692927207 | *m**: *(+39) 3408816643 | *e: *
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>
â

Jeff Squyres (jsquyres)

2016-05-06 12:10:58 UTC

Permalink

Ok, good.

I asked that question because typically when we see errors like this, it is usually either a busted compiler installation or inadvertently mixing the run-times of multiple different compilers in some kind of incompatible way. Specifically, the mpifort (aka mpif90) application is a fairly simple program -- there's no reason it should segv, especially with a stack trace that you sent that implies that it's dying early in startup, potentially even before it has hit any Open MPI code (i.e., it could even be pre-main).

BTW, you might be able to get a more complete stack trace from the debugger that comes with the Intel compiler (idb? I don't remember offhand).

Since you are able to run simple programs compiled by this compiler, it sounds like the compiler is working fine. Good!

The next thing to check is to see if somehow the compiler and/or run-time environments are getting mixed up. E.g., the apps were compiled for one compiler/run-time but are being used with another. Also ensure that any compiler/linker flags that you are passing to Open MPI's configure script are native and correct for the platform for which you're compiling (e.g., don't pass in flags that optimize for a different platform; that may result in generating machine code instructions that are invalid for your platform).

Try recompiling/re-installing Open MPI from scratch, and if it still doesn't work, then send all the information listed here:

https://www.open-mpi.org/community/help/

Yes, I've tried three simple "Hello world" programs in fortan, C and C++ and the compile and run with intel 16.0.3. The problem is with the openmpi compiled from source.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza" University of Rome
Member of Fortran-FOSS-programmers
gdb /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
GNU gdb (GDB) 7.11
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-pc-linux-gnu".
Type "show configuration" for configuration details.
<http://www.gnu.org/software/gdb/bugs/>.
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90...(no debugging symbols found)...done.
(gdb) r -v
Starting program: /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff6858f38 in ?? ()
(gdb) bt
#0 0x00007ffff6858f38 in ?? ()
#1 0x00007ffff7de5828 in _dl_relocate_object () from /lib64/ld-linux-x86-64.so.2
#2 0x00007ffff7ddcfa3 in dl_main () from /lib64/ld-linux-x86-64.so.2
#3 0x00007ffff7df029c in _dl_sysdep_start () from /lib64/ld-linux-x86-64.so.2
#4 0x00007ffff7dddd4a in _dl_start () from /lib64/ld-linux-x86-64.so.2
#5 0x00007ffff7dd9d98 in _start () from /lib64/ld-linux-x86-64.so.2
#6 0x0000000000000002 in ?? ()
#7 0x00007fffffffaa8a in ?? ()
#8 0x00007fffffffaab6 in ?? ()
#9 0x0000000000000000 in ?? ()
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza" University of Rome
Member of Fortran-FOSS-programmers
'ldd /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
linux-vdso.so.1 (0x00007ffcacbbe000)
libopen-pal.so.13 => /opt/openmpi/1.10.2/intel/16.0.3/lib/libopen-pal.so.13 (0x00007fa9597a9000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007fa9594a4000)
libpciaccess.so.0 => /usr/lib/libpciaccess.so.0 (0x00007fa95929a000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fa959096000)
librt.so.1 => /usr/lib/librt.so.1 (0x00007fa958e8e000)
libutil.so.1 => /usr/lib/libutil.so.1 (0x00007fa958c8b000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fa958a75000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fa958858000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007fa9584b7000)
libimf.so => /home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libimf.so (0x00007fa957fb9000)
libsvml.so => /home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libsvml.so (0x00007fa9570ad000)
libirng.so => /home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libirng.so (0x00007fa956d3b000)
libintlc.so.5 => /home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libintlc.so.5 (0x00007fa956acf000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa959ab9000)'
I can't provide a core file, because I can't compile or launch any program with mpifort... I've always the error 'core dumped' also when I try to compile a program with mpifort, and of course there isn't any core file.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza" University of Rome
Member of Fortran-FOSS-programmers
I’ve installed the latest version of Intel Parallel Studio (16.0.3), then I’ve downloaded the latest version of openmpi (1.10.2) and I’ve compiled it with
`./configure CC=icc CXX=icpc F77=ifort FC=ifort --prefix=/opt/openmpi/1.10.2/intel/16.0.3`
then I've installed and everything seems ok, but when I try the simple command
' /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v'
I receive the following error
'Segmentation fault (core dumped)'
I'm on ArchLinux, with kernel 4.5.1-1-ARCH; I've attache to this email the config.log file compressed with bzip2.
Any help will be appreciated!
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza" University of Rome
Member of Fortran-FOSS-programmers
_______________________________________________
users mailing list
Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users
Link to this post: http://www.open-mpi.org/community/lists/users/2016/05/29108.php

--
Jeff Squyres
***@cisco.com
For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/

Paul Kapinos

2016-12-14 12:29:57 UTC

Permalink

Hello all,
we seem to run into the same issue: 'mpif90' sigsegvs immediately for Open MPI
1.10.4 compiled using Intel compilers 16.0.4.258 and 16.0.3.210, while it works
fine when compiled with 16.0.2.181.

It seems to be a compiler issue (more exactly: library issue on libs delivered
with 16.0.4.258 and 16.0.3.210 versions). Changing the version of compiler
loaded back to 16.0.2.181 (=> change of dynamically loaded libs) let the
prevously-failing binary (compiled with newer compilers) to work propperly.

Compiling with -O0 does not help. As the issue is likely in the Intel libs (as
said changing out these solves/raises the issue) we will do a failback to
16.0.2.181 compiler version. We will try to open a case by Intel - let's see...

Have a nice day,

Paul Kapinos

Post by Jeff Squyres (jsquyres)
Ok, good.
I asked that question because typically when we see errors like this, it is usually either a busted compiler installation or inadvertently mixing the run-times of multiple different compilers in some kind of incompatible way. Specifically, the mpifort (aka mpif90) application is a fairly simple program -- there's no reason it should segv, especially with a stack trace that you sent that implies that it's dying early in startup, potentially even before it has hit any Open MPI code (i.e., it could even be pre-main).
BTW, you might be able to get a more complete stack trace from the debugger that comes with the Intel compiler (idb? I don't remember offhand).
Since you are able to run simple programs compiled by this compiler, it sounds like the compiler is working fine. Good!
The next thing to check is to see if somehow the compiler and/or run-time environments are getting mixed up. E.g., the apps were compiled for one compiler/run-time but are being used with another. Also ensure that any compiler/linker flags that you are passing to Open MPI's configure script are native and correct for the platform for which you're compiling (e.g., don't pass in flags that optimize for a different platform; that may result in generating machine code instructions that are invalid for your platform).
https://www.open-mpi.org/community/help/

Yes, I've tried three simple "Hello world" programs in fortan, C and C++ and the compile and run with intel 16.0.3. The problem is with the openmpi compiled from source.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza" University of Rome
Member of Fortran-FOSS-programmers
gdb /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
GNU gdb (GDB) 7.11
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-pc-linux-gnu".
Type "show configuration" for configuration details.
<http://www.gnu.org/software/gdb/bugs/>.
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90...(no debugging symbols found)...done.
(gdb) r -v
Starting program: /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff6858f38 in ?? ()
(gdb) bt
#0 0x00007ffff6858f38 in ?? ()
#1 0x00007ffff7de5828 in _dl_relocate_object () from /lib64/ld-linux-x86-64.so.2
#2 0x00007ffff7ddcfa3 in dl_main () from /lib64/ld-linux-x86-64.so.2
#3 0x00007ffff7df029c in _dl_sysdep_start () from /lib64/ld-linux-x86-64.so.2
#4 0x00007ffff7dddd4a in _dl_start () from /lib64/ld-linux-x86-64.so.2
#5 0x00007ffff7dd9d98 in _start () from /lib64/ld-linux-x86-64.so.2
#6 0x0000000000000002 in ?? ()
#7 0x00007fffffffaa8a in ?? ()
#8 0x00007fffffffaab6 in ?? ()
#9 0x0000000000000000 in ?? ()
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza" University of Rome
Member of Fortran-FOSS-programmers
'ldd /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
linux-vdso.so.1 (0x00007ffcacbbe000)
libopen-pal.so.13 => /opt/openmpi/1.10.2/intel/16.0.3/lib/libopen-pal.so.13 (0x00007fa9597a9000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007fa9594a4000)
libpciaccess.so.0 => /usr/lib/libpciaccess.so.0 (0x00007fa95929a000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fa959096000)
librt.so.1 => /usr/lib/librt.so.1 (0x00007fa958e8e000)
libutil.so.1 => /usr/lib/libutil.so.1 (0x00007fa958c8b000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fa958a75000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fa958858000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007fa9584b7000)
libimf.so => /home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libimf.so (0x00007fa957fb9000)
libsvml.so => /home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libsvml.so (0x00007fa9570ad000)
libirng.so => /home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libirng.so (0x00007fa956d3b000)
libintlc.so.5 => /home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libintlc.so.5 (0x00007fa956acf000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa959ab9000)'
I can't provide a core file, because I can't compile or launch any program with mpifort... I've always the error 'core dumped' also when I try to compile a program with mpifort, and of course there isn't any core file.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza" University of Rome
Member of Fortran-FOSS-programmers
Iâve installed the latest version of Intel Parallel Studio (16.0.3), then Iâve downloaded the latest version of openmpi (1.10.2) and Iâve compiled it with
`./configure CC=icc CXX=icpc F77=ifort FC=ifort --prefix=/opt/openmpi/1.10.2/intel/16.0.3`
then I've installed and everything seems ok, but when I try the simple command
' /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v'
I receive the following error
'Segmentation fault (core dumped)'
I'm on ArchLinux, with kernel 4.5.1-1-ARCH; I've attache to this email the config.log file compressed with bzip2.
Any help will be appreciated!
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza" University of Rome
Member of Fortran-FOSS-programmers
_______________________________________________
users mailing list
Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users
Link to this post: http://www.open-mpi.org/community/lists/users/2016/05/29108.php

--
Dipl.-Inform. Paul Kapinos - High Performance Computing,
RWTH Aachen University, IT Center
Seffenter Weg 23, D 52074 Aachen (Germany)
Tel: +49 241/80-24915

Paul Kapinos

2016-12-23 10:41:40 UTC

Permalink

Hi all,

we discussed this issue with Intel compiler support and it looks like they now
know what the issue is and how to protect after. It is a known issue resulting
from a backwards incompatibility in an OS/glibc update, cf.
https://sourceware.org/bugzilla/show_bug.cgi?id=20019

Affected versions of the Intel compilers: 16.0.3, 16.0.4
Not affected versions: 16.0.2, 17.0

So, simply do not use affected versions (and hope on an bugfix update in 16x
series if you cannot immediately upgrade to 17x, like we, despite this is the
favourite option from Intel).

Have a nice Christmas time!

Paul Kapinos

Post by Paul Kapinos
Hello all,
we seem to run into the same issue: 'mpif90' sigsegvs immediately for Open MPI
1.10.4 compiled using Intel compilers 16.0.4.258 and 16.0.3.210, while it works
fine when compiled with 16.0.2.181.
It seems to be a compiler issue (more exactly: library issue on libs delivered
with 16.0.4.258 and 16.0.3.210 versions). Changing the version of compiler
loaded back to 16.0.2.181 (=> change of dynamically loaded libs) let the
prevously-failing binary (compiled with newer compilers) to work propperly.
Compiling with -O0 does not help. As the issue is likely in the Intel libs (as
said changing out these solves/raises the issue) we will do a failback to
16.0.2.181 compiler version. We will try to open a case by Intel - let's see...
Have a nice day,
Paul Kapinos

Post by Jeff Squyres (jsquyres)
Ok, good.
I asked that question because typically when we see errors like this, it is
usually either a busted compiler installation or inadvertently mixing the
run-times of multiple different compilers in some kind of incompatible way.
Specifically, the mpifort (aka mpif90) application is a fairly simple program
-- there's no reason it should segv, especially with a stack trace that you
sent that implies that it's dying early in startup, potentially even before it
has hit any Open MPI code (i.e., it could even be pre-main).
BTW, you might be able to get a more complete stack trace from the debugger
that comes with the Intel compiler (idb? I don't remember offhand).
Since you are able to run simple programs compiled by this compiler, it sounds
like the compiler is working fine. Good!
The next thing to check is to see if somehow the compiler and/or run-time
environments are getting mixed up. E.g., the apps were compiled for one
compiler/run-time but are being used with another. Also ensure that any
compiler/linker flags that you are passing to Open MPI's configure script are
native and correct for the platform for which you're compiling (e.g., don't
pass in flags that optimize for a different platform; that may result in
generating machine code instructions that are invalid for your platform).
Try recompiling/re-installing Open MPI from scratch, and if it still doesn't
https://www.open-mpi.org/community/help/

Yes, I've tried three simple "Hello world" programs in fortan, C and C++ and
the compile and run with intel 16.0.3. The problem is with the openmpi
compiled from source.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
Member of Fortran-FOSS-programmers
gdb /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
GNU gdb (GDB) 7.11
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-pc-linux-gnu".
Type "show configuration" for configuration details.
<http://www.gnu.org/software/gdb/bugs/>.
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90...(no
debugging symbols found)...done.
(gdb) r -v
Starting program: /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff6858f38 in ?? ()
(gdb) bt
#0 0x00007ffff6858f38 in ?? ()
#1 0x00007ffff7de5828 in _dl_relocate_object () from
/lib64/ld-linux-x86-64.so.2
#2 0x00007ffff7ddcfa3 in dl_main () from /lib64/ld-linux-x86-64.so.2
#3 0x00007ffff7df029c in _dl_sysdep_start () from /lib64/ld-linux-x86-64.so.2
#4 0x00007ffff7dddd4a in _dl_start () from /lib64/ld-linux-x86-64.so.2
#5 0x00007ffff7dd9d98 in _start () from /lib64/ld-linux-x86-64.so.2
#6 0x0000000000000002 in ?? ()
#7 0x00007fffffffaa8a in ?? ()
#8 0x00007fffffffaab6 in ?? ()
#9 0x0000000000000000 in ?? ()
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
Member of Fortran-FOSS-programmers
'ldd /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
linux-vdso.so.1 (0x00007ffcacbbe000)
libopen-pal.so.13 =>
/opt/openmpi/1.10.2/intel/16.0.3/lib/libopen-pal.so.13 (0x00007fa9597a9000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007fa9594a4000)
libpciaccess.so.0 => /usr/lib/libpciaccess.so.0 (0x00007fa95929a000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fa959096000)
librt.so.1 => /usr/lib/librt.so.1 (0x00007fa958e8e000)
libutil.so.1 => /usr/lib/libutil.so.1 (0x00007fa958c8b000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fa958a75000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fa958858000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007fa9584b7000)
libimf.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libimf.so
(0x00007fa957fb9000)
libsvml.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libsvml.so
(0x00007fa9570ad000)
libirng.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libirng.so
(0x00007fa956d3b000)
libintlc.so.5 =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libintlc.so.5
(0x00007fa956acf000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa959ab9000)'
I can't provide a core file, because I can't compile or launch any program
with mpifort... I've always the error 'core dumped' also when I try to
compile a program with mpifort, and of course there isn't any core file.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
Member of Fortran-FOSS-programmers
Iâve installed the latest version of Intel Parallel Studio (16.0.3), then
Iâve downloaded the latest version of openmpi (1.10.2) and Iâve compiled it with
`./configure CC=icc CXX=icpc F77=ifort FC=ifort
--prefix=/opt/openmpi/1.10.2/intel/16.0.3`
then I've installed and everything seems ok, but when I try the simple command
' /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v'
I receive the following error
'Segmentation fault (core dumped)'
I'm on ArchLinux, with kernel 4.5.1-1-ARCH; I've attache to this email the
config.log file compressed with bzip2.
Any help will be appreciated!
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
Member of Fortran-FOSS-programmers
_______________________________________________
users mailing list
Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users
http://www.open-mpi.org/community/lists/users/2016/05/29108.php

--
Dipl.-Inform. Paul Kapinos - High Performance Computing,
RWTH Aachen University, IT Center
Seffenter Weg 23, D 52074 Aachen (Germany)
Tel: +49 241/80-24915

Howard Pritchard

2016-12-23 18:11:11 UTC

Permalink

Hi Paul,

Thanks very much Christmas present.

The Open MPI README has been updated
to include a note about issues with the Intel 16.0.3-4 compiler suites.

Enjoy the holidays,

Howard

Post by Paul Kapinos
Hi all,
we discussed this issue with Intel compiler support and it looks like they
now know what the issue is and how to protect after. It is a known issue
resulting from a backwards incompatibility in an OS/glibc update, cf.
https://sourceware.org/bugzilla/show_bug.cgi?id=20019
Affected versions of the Intel compilers: 16.0.3, 16.0.4
Not affected versions: 16.0.2, 17.0
So, simply do not use affected versions (and hope on an bugfix update in
16x series if you cannot immediately upgrade to 17x, like we, despite this
is the favourite option from Intel).
Have a nice Christmas time!
Paul Kapinos

Post by Jeff Squyres (jsquyres)
Ok, good.
I asked that question because typically when we see errors like this, it is
usually either a busted compiler installation or inadvertently mixing the
run-times of multiple different compilers in some kind of incompatible way.
Specifically, the mpifort (aka mpif90) application is a fairly simple program
-- there's no reason it should segv, especially with a stack trace that you
sent that implies that it's dying early in startup, potentially even before it
has hit any Open MPI code (i.e., it could even be pre-main).
BTW, you might be able to get a more complete stack trace from the debugger
that comes with the Intel compiler (idb? I don't remember offhand).
Since you are able to run simple programs compiled by this compiler, it sounds
like the compiler is working fine. Good!
The next thing to check is to see if somehow the compiler and/or run-time
environments are getting mixed up. E.g., the apps were compiled for one
compiler/run-time but are being used with another. Also ensure that any
compiler/linker flags that you are passing to Open MPI's configure script are
native and correct for the platform for which you're compiling (e.g., don't
pass in flags that optimize for a different platform; that may result in
generating machine code instructions that are invalid for your platform).
Try recompiling/re-installing Open MPI from scratch, and if it still doesn't
https://www.open-mpi.org/community/help/

Yes, I've tried three simple "Hello world" programs in fortan, C and C++ and
the compile and run with intel 16.0.3. The problem is with the openmpi
compiled from source.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
Member of Fortran-FOSS-programmers
gdb /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
GNU gdb (GDB) 7.11
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <
http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-pc-linux-gnu".
Type "show configuration" for configuration details.
<http://www.gnu.org/software/gdb/bugs/>.
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90...(no
debugging symbols found)...done.
(gdb) r -v
Starting program: /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff6858f38 in ?? ()
(gdb) bt
#0 0x00007ffff6858f38 in ?? ()
#1 0x00007ffff7de5828 in _dl_relocate_object () from
/lib64/ld-linux-x86-64.so.2
#2 0x00007ffff7ddcfa3 in dl_main () from /lib64/ld-linux-x86-64.so.2
#3 0x00007ffff7df029c in _dl_sysdep_start () from
/lib64/ld-linux-x86-64.so.2
#4 0x00007ffff7dddd4a in _dl_start () from /lib64/ld-linux-x86-64.so.2
#5 0x00007ffff7dd9d98 in _start () from /lib64/ld-linux-x86-64.so.2
#6 0x0000000000000002 in ?? ()
#7 0x00007fffffffaa8a in ?? ()
#8 0x00007fffffffaab6 in ?? ()
#9 0x0000000000000000 in ?? ()
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
Member of Fortran-FOSS-programmers
'ldd /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
linux-vdso.so.1 (0x00007ffcacbbe000)
libopen-pal.so.13 =>
/opt/openmpi/1.10.2/intel/16.0.3/lib/libopen-pal.so.13
(0x00007fa9597a9000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007fa9594a4000)
libpciaccess.so.0 => /usr/lib/libpciaccess.so.0 (0x00007fa95929a000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fa959096000)
librt.so.1 => /usr/lib/librt.so.1 (0x00007fa958e8e000)
libutil.so.1 => /usr/lib/libutil.so.1 (0x00007fa958c8b000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fa958a75000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fa958858000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007fa9584b7000)
libimf.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux
/compiler/lib/intel64/libimf.so
(0x00007fa957fb9000)
libsvml.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux
/compiler/lib/intel64/libsvml.so
(0x00007fa9570ad000)
libirng.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux
/compiler/lib/intel64/libirng.so
(0x00007fa956d3b000)
libintlc.so.5 =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux
/compiler/lib/intel64/libintlc.so.5
(0x00007fa956acf000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa959ab9000)'
I can't provide a core file, because I can't compile or launch any program
with mpifort... I've always the error 'core dumped' also when I try to
compile a program with mpifort, and of course there isn't any core file.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
Member of Fortran-FOSS-programmers
Iâve installed the latest version of Intel Parallel Studio (16.0.3), then
Iâve downloaded the latest version of openmpi (1.10.2) and Iâve
compiled it with
`./configure CC=icc CXX=icpc F77=ifort FC=ifort
--prefix=/opt/openmpi/1.10.2/intel/16.0.3`
then I've installed and everything seems ok, but when I try the simple command
' /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v'
I receive the following error
'Segmentation fault (core dumped)'
I'm on ArchLinux, with kernel 4.5.1-1-ARCH; I've attache to this email the
config.log file compressed with bzip2.
Any help will be appreciated!
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
Member of Fortran-FOSS-programmers
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Giacomo Rossi

2016-05-09 10:50:06 UTC

Permalink

I've send you all the outputs from configure, make and make install
commands...

Today I've compiled openmpi with the latest gcc version (6.1.1) shipped
with my archlinux distro and everything seems ok, so I think that the
problem is with intel compiler.

Giacomo Rossi Ph.D., Space Engineer

Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
*p: *(+39) 0692927207 | *m**: *(+39) 3408816643 | *e: ****@gmail.com
<***@uniroma1.it>
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>

Post by Giacomo Rossi
Yes, I've tried three simple "Hello world" programs in fortan, C and C++
and the compile and run with intel 16.0.3. The problem is with the openmpi
compiled from source.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>

Post by Giacomo Rossi
'ldd /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90
linux-vdso.so.1 (0x00007ffcacbbe000)
libopen-pal.so.13 =>
/opt/openmpi/1.10.2/intel/16.0.3/lib/libopen-pal.so.13 (0x00007fa9597a9000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007fa9594a4000)
libpciaccess.so.0 => /usr/lib/libpciaccess.so.0 (0x00007fa95929a000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fa959096000)
librt.so.1 => /usr/lib/librt.so.1 (0x00007fa958e8e000)
libutil.so.1 => /usr/lib/libutil.so.1 (0x00007fa958c8b000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fa958a75000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fa958858000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007fa9584b7000)
libimf.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libimf.so
(0x00007fa957fb9000)
libsvml.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libsvml.so
(0x00007fa9570ad000)
libirng.so =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libirng.so
(0x00007fa956d3b000)
libintlc.so.5 =>
/home/giacomo/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libintlc.so.5
(0x00007fa956acf000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa959ab9000)'
I can't provide a core file, because I can't compile or launch any
program with mpifort... I've always the error 'core dumped' also when I try
to compile a program with mpifort, and of course there isn't any core file.
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
*p: *(+39) 0692927207 | *m**: *(+39) 3408816643 | *e: *
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>

Post by Giacomo Rossi
Iâve installed the latest version of Intel Parallel Studio (16.0.3),
then Iâve downloaded the latest version of openmpi (1.10.2) and Iâve
compiled it with
`./configure CC=icc CXX=icpc F77=ifort FC=ifort
--prefix=/opt/openmpi/1.10.2/intel/16.0.3`
then I've installed and everything seems ok, but when I try the simple
command
' /opt/openmpi/1.10.2/intel/16.0.3/bin/mpif90 -v'
I receive the following error
'Segmentation fault (core dumped)'
I'm on ArchLinux, with kernel 4.5.1-1-ARCH; I've attache to this email
the config.log file compressed with bzip2.
Any help will be appreciated!
Giacomo Rossi Ph.D., Space Engineer
Research Fellow at Dept. of Mechanical and Aerospace Engineering, "Sapienza"
University of Rome
*p: *(+39) 0692927207 | *m**: *(+39) 3408816643 | *e: *
Member of Fortran-FOSS-programmers
<https://github.com/Fortran-FOSS-Programmers>
â