[Wien] SIGBUS occurred in lapw1 on RHEL6.2

Wed Jun 20 03:54:34 CEST 2012

Thank you for your reply.

>Which version are you using?

We installed Cluster Studio XE as Intel compiler.
Its version is composer_xe_2011_sp1.6.233.
$ ifort -v
ifort version 12.1.0
$ ./getversion.out
Intel(R) Math Kernel Library Version 10.3.6 Product Build 20110809 for 
Intel(R) 64 architecture applications

My RHEL5.5 machine, on which I could run wien2k without error, is
$ ifort -v
Version 12.0.2
$ ./getversion.out
Intel(R) Math Kernel Library Version 10.3.2 Product Build 20110112 for 
Intel(R) 64 architecture applications
composer's version is composerxe-2011.2.137.

Thanks
N.Igarashi

Laurence Marks wrote:

> 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
> >
> >
> >
> >
> > _______________________________________________
> > 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