[Wien] SIGBUS occurred in lapw1 on RHEL6.2

Laurence Marks L-marks at northwestern.edu
Wed Jun 20 04:31:09 CEST 2012 

Please check the build version details against what is in the message link
I sent.
On Jun 19, 2012 8:55 PM, "Nobuaki Igarashi" <igarashi at imr.tohoku.ac.jp>
wrote:

> 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.htmlsuggests
> > >> 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
>
>
>
>
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