[Wien] SIGBUS occurred in lapw1 on RHEL6.2

[Nobuaki Igarashi]

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
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