[Wien] SIGBUS occurred in lapw1 on RHEL6.2

[Laurence Marks]

Did you search the mailing list for ifort versions -- several are
buggy, see http://zeus.theochem.tuwien.ac.at/pipermail/wien/2011-November/015682.html
as well as earlier emails.

Which version are you using?

On Tue, Jun 19, 2012 at 7:16 PM, Nobuaki Igarashi
<igarashi at imr.tohoku.ac.jp> wrote:
> Thank you for your quick reply.
>
> Regarding "Bug 11357 - SIGBUS in getenv(). ", I've already check.
> But it seems problem of the programing method.
>
> I removed " -warn nogeneral  -g -openmp -static-libgcc".
> (I set the option "-static-libgcc" to copy the executables compiled on
> RHEL5.5.)
> The "-i-static" option has already been deprecated currently, ifort tells us
> to use -static-intel instead.
>
> I compiled all modules with
> "-free -w -mp1 -prec-div -pc80 -DINTEL_VML -traceback -static-intel".
> However, now, SIGSEGV occurred in openmp library.
>
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image              PC                Routine            Line        Source
> libiomp5.so        00007F77009F4A5A  Unknown               Unknown  Unknown
> libiomp5.so        00007F77009E128C  Unknown               Unknown  Unknown
> libiomp5.so        00007F77009DDBB0  Unknown               Unknown  Unknown
> libiomp5.so        00007F77009DD238  Unknown               Unknown  Unknown
> libiomp5.so        00007F77009FAEBB  Unknown               Unknown  Unknown
> libpthread.so.0    000000379F4077F1  Unknown               Unknown  Unknown
> libc.so.6          000000379F0E5CCD  Unknown               Unknown  Unknown
>
> Thanks
> N.Igarashi
>
> Laurence Marks wrote:
>
>> A google search on "sigbus getenv", for instance
>> http://sources.redhat.com/ml/glibc-bugs/2010-03/msg00005.html suggests
>> that this might be a known bug. I think you will have to try various
>> things until they work. Some ideas:
>>
>> a) Check against the mailing list archive to see if there any other
>> reports of bugs with this version of ifort. Of late there have been
>> problems.
>> b) remove " -warn nogeneral  -g -openmp -static-libgcc". I don't think
>> -g is a good idea except when writing code, and I do not believe
>> Wien2k currently uses openmp anywhere, everything is blas.
>> c) If this does not work, also remove "-pad"
>> d) If this does not work, add "-i-static".
>>
>> On Sun, Jun 17, 2012 at 6:54 PM, Nobuaki Igarashi
>> <igarashi at imr.tohoku.ac.jp> wrote:
>> > Dear developers and WIEN2k users,
>> >
>> > Although I completed compiling WIEN2k along siteconfig procedure, lapw1
>> > was abnormally ended as soon as it started by SIGBUS.
>> >
>> > The following is the debugger's output.
>> > (idb) run
>> > Starting program: /home007/lacse/my_wien2k/wien2k.org/lapw1
>> > [New Thread 8144 (LWP 8144)]
>> > Program received signal SIGBUS
>> > getenv () in /lib64/libc-2.12.so
>> > (idb) where
>> > #0 ?0x000000332c4352c0 in getenv () in /lib64/libc-2.12.so
>> > #1 ?0x0000000000488288 in for_check_env_name () in
>> > /home007/lacse/my_wien2k/wien2k.org/lapw1
>> > #2 ?0x00000000004ccfa2 in for__open_proc () in
>> > /home007/lacse/my_wien2k/wien2k.org/lapw1
>> > #3 ?0x000000000048d908 in for_open () in
>> > /home007/lacse/my_wien2k/wien2k.org/lapw1
>> > #4 ?0x00000000004184f3 in errclr (fname=(...)) at
>> > /home007/lacse/my_wien2k/wien2k.org/SRC_lapw1/errclr.f:64
>> > #5 ?0x0000000000443e92 in lapw1 () at
>> > /home007/lacse/my_wien2k/wien2k.org/SRC_lapw1/lapw1_tmp_.F:90
>> > #6 ?0x0000000000404c5c in main () in
>> > /home007/lacse/my_wien2k/wien2k.org/lapw1
>> > #7 ?0x000000332c41ecdd in __libc_start_main () in /lib64/libc-2.12.so
>> >
>> > This issue occurred on only RHEL 6.2, there is no problem on RHEL5.5.
>> > Now, I compiled WIEN2k with -static-libgc, which is one of options of Intel
>> > compiler, on RHEL5.5,
>> > I copied it to new server. ?Then, no error occurred.
>> >
>> > Although it may come from a problem of glibc of RHEL 6.2,
>> > had you had such a information, yet?
>> > If you know regarding this, please let me know anything.
>> >
>> > -----------------------------------------------------------------------
>> > I write our system informations :
>> >
>> > [The new system ]
>> > IBM BladeCenter HS22
>> > Operating System : Red Hat Enterprise Linux ComputeNode release 6.2
>> > (Santiago)
>> > CPU model : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
>> > CPU cores : 12
>> > Memory : 24594924kB (free 14196424kB)
>> > Kernel : Linux 2.6.32-220.7.1.el6
>> > GLIBC : GNU C Library stable release version 2.12, by Roland McGrath et al.
>> >
>> > [RHEL 5.5 Systems]
>> > IBM iDataPlex dx360
>> > Operating System : Red Hat Enterprise Linux Server release 5.5 (Tikanga)
>> > CPU model : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
>> > CPU cores : 12
>> > Memory : 24GB
>> > Kernel : Linux ?2.6.18-194.26.1.el5
>> > GLIBC : GNU C Library stable release version 2.5, by Roland McGrath et al.
>> >
>> > [Compiler]
>> > ifort version 12.1.0
>> > Intel(R) Math Kernel Library Version 10.3.6 Product Build 20110809 for
>> > Intel(R) 64 architecture applications
>> >
>> > [WIEN2k Compile options]
>> > WIEN2k version : WIEN2k_11.1
>> > FOPT:-free -mp1 -warn
>> > nogeneral -prec-div -pc80 -pad -ip -DINTEL_VML -traceback -g -openmp -static-libgcc
>> > current:LDFLAGS:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -static-libgcc
>> > DPARALLEL:'-DParallel'
>> > R_LIBS:$(MKLROOT)/lib/intel64/libmkl_blas95_lp64.a
>> > $(MKLROOT)/lib/intel64/libmkl_lapack95_lp64.a \
>> > -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a \
>> > $(MKLROOT)/lib/intel64/libmkl_intel_thread.a
>> > $(MKLROOT)/lib/intel64/libmkl_core.a \
>> > -Wl,--end-group -openmp -lpthread -lm
>> >
>> > * Not MPI version, but MKL + OpenMP version
>> >
>> > Thanks in advance.
>> > N.Igarashi
>> >
>> >
>> >
>> > _______________________________________________
>> > Wien mailing list
>> > Wien at zeus.theochem.tuwien.ac.at
>> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>
>>
>>
>> --
>> Professor Laurence Marks
>> Department of Materials Science and Engineering
>> Northwestern University
>> www.numis.northwestern.edu 1-847-491-3996
>> "Research is to see what everybody else has seen, and to think what
>> nobody else has thought"
>> Albert Szent-Gyorgi
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>
>
>
>
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-- 
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu 1-847-491-3996
"Research is to see what everybody else has seen, and to think what
nobody else has thought"
Albert Szent-Gyorgi