<p>Please check the build version details against what is in the message link I sent.</p>
<div class="gmail_quote">On Jun 19, 2012 8:55 PM, "Nobuaki Igarashi" <<a href="mailto:igarashi@imr.tohoku.ac.jp">igarashi@imr.tohoku.ac.jp</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thank you for your reply.<br>
<br>
>Which version are you using?<br>
<br>
We installed Cluster Studio XE as Intel compiler.<br>
Its version is composer_xe_2011_sp1.6.233.<br>
$ ifort -v<br>
ifort version 12.1.0<br>
$ ./getversion.out<br>
Intel(R) Math Kernel Library Version 10.3.6 Product Build 20110809 for<br>
Intel(R) 64 architecture applications<br>
<br>
My RHEL5.5 machine, on which I could run wien2k without error, is<br>
$ ifort -v<br>
Version 12.0.2<br>
$ ./getversion.out<br>
Intel(R) Math Kernel Library Version 10.3.2 Product Build 20110112 for<br>
Intel(R) 64 architecture applications<br>
composer's version is composerxe-2011.2.137.<br>
<br>
Thanks<br>
N.Igarashi<br>
<br>
Laurence Marks wrote:<br>
<br>
> Did you search the mailing list for ifort versions -- several are<br>
> buggy, see <a href="http://zeus.theochem.tuwien.ac.at/pipermail/wien/2011-November/015682.html" target="_blank">http://zeus.theochem.tuwien.ac.at/pipermail/wien/2011-November/015682.html</a><br>
> as well as earlier emails.<br>
><br>
> Which version are you using?<br>
><br>
> On Tue, Jun 19, 2012 at 7:16 PM, Nobuaki Igarashi<br>
> <<a href="mailto:igarashi@imr.tohoku.ac.jp">igarashi@imr.tohoku.ac.jp</a>> wrote:<br>
> > Thank you for your quick reply.<br>
> ><br>
> > Regarding "Bug 11357 - SIGBUS in getenv(). ", I've already check.<br>
> > But it seems problem of the programing method.<br>
> ><br>
> > I removed " -warn nogeneral ?-g -openmp -static-libgcc".<br>
> > (I set the option "-static-libgcc" to copy the executables compiled on<br>
> > RHEL5.5.)<br>
> > The "-i-static" option has already been deprecated currently, ifort tells us<br>
> > to use -static-intel instead.<br>
> ><br>
> > I compiled all modules with<br>
> > "-free -w -mp1 -prec-div -pc80 -DINTEL_VML -traceback -static-intel".<br>
> > However, now, SIGSEGV occurred in openmp library.<br>
> ><br>
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred<br>
> > Image ? ? ? ? ? ? ?PC ? ? ? ? ? ? ? ?Routine ? ? ? ? ? ?Line ? ? ? ?Source<br>
> > libiomp5.so ? ? ? ?00007F77009F4A5A ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown<br>
> > libiomp5.so ? ? ? ?00007F77009E128C ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown<br>
> > libiomp5.so ? ? ? ?00007F77009DDBB0 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown<br>
> > libiomp5.so ? ? ? ?00007F77009DD238 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown<br>
> > libiomp5.so ? ? ? ?00007F77009FAEBB ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown<br>
> > libpthread.so.0 ? ?000000379F4077F1 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown<br>
> > libc.so.6 ? ? ? ? ?000000379F0E5CCD ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown<br>
> ><br>
> > Thanks<br>
> > N.Igarashi<br>
> ><br>
> > Laurence Marks wrote:<br>
> ><br>
> >> A google search on "sigbus getenv", for instance<br>
> >> <a href="http://sources.redhat.com/ml/glibc-bugs/2010-03/msg00005.html" target="_blank">http://sources.redhat.com/ml/glibc-bugs/2010-03/msg00005.html</a> suggests<br>
> >> that this might be a known bug. I think you will have to try various<br>
> >> things until they work. Some ideas:<br>
> >><br>
> >> a) Check against the mailing list archive to see if there any other<br>
> >> reports of bugs with this version of ifort. Of late there have been<br>
> >> problems.<br>
> >> b) remove " -warn nogeneral ?-g -openmp -static-libgcc". I don't think<br>
> >> -g is a good idea except when writing code, and I do not believe<br>
> >> Wien2k currently uses openmp anywhere, everything is blas.<br>
> >> c) If this does not work, also remove "-pad"<br>
> >> d) If this does not work, add "-i-static".<br>
> >><br>
> >> On Sun, Jun 17, 2012 at 6:54 PM, Nobuaki Igarashi<br>
> >> <<a href="mailto:igarashi@imr.tohoku.ac.jp">igarashi@imr.tohoku.ac.jp</a>> wrote:<br>
> >> > Dear developers and WIEN2k users,<br>
> >> ><br>
> >> > Although I completed compiling WIEN2k along siteconfig procedure, lapw1<br>
> >> > was abnormally ended as soon as it started by SIGBUS.<br>
> >> ><br>
> >> > The following is the debugger's output.<br>
> >> > (idb) run<br>
> >> > Starting program: /home007/lacse/my_wien2k/<a href="http://wien2k.org/lapw1" target="_blank">wien2k.org/lapw1</a><br>
> >> > [New Thread 8144 (LWP 8144)]<br>
> >> > Program received signal SIGBUS<br>
> >> > getenv () in /lib64/<a href="http://libc-2.12.so" target="_blank">libc-2.12.so</a><br>
> >> > (idb) where<br>
> >> > #0 ?0x000000332c4352c0 in getenv () in /lib64/<a href="http://libc-2.12.so" target="_blank">libc-2.12.so</a><br>
> >> > #1 ?0x0000000000488288 in for_check_env_name () in<br>
> >> > /home007/lacse/my_wien2k/<a href="http://wien2k.org/lapw1" target="_blank">wien2k.org/lapw1</a><br>
> >> > #2 ?0x00000000004ccfa2 in for__open_proc () in<br>
> >> > /home007/lacse/my_wien2k/<a href="http://wien2k.org/lapw1" target="_blank">wien2k.org/lapw1</a><br>
> >> > #3 ?0x000000000048d908 in for_open () in<br>
> >> > /home007/lacse/my_wien2k/<a href="http://wien2k.org/lapw1" target="_blank">wien2k.org/lapw1</a><br>
> >> > #4 ?0x00000000004184f3 in errclr (fname=(...)) at<br>
> >> > /home007/lacse/my_wien2k/<a href="http://wien2k.org/SRC_lapw1/errclr.f:64" target="_blank">wien2k.org/SRC_lapw1/errclr.f:64</a><br>
> >> > #5 ?0x0000000000443e92 in lapw1 () at<br>
> >> > /home007/lacse/my_wien2k/<a href="http://wien2k.org/SRC_lapw1/lapw1_tmp_.F:90" target="_blank">wien2k.org/SRC_lapw1/lapw1_tmp_.F:90</a><br>
> >> > #6 ?0x0000000000404c5c in main () in<br>
> >> > /home007/lacse/my_wien2k/<a href="http://wien2k.org/lapw1" target="_blank">wien2k.org/lapw1</a><br>
> >> > #7 ?0x000000332c41ecdd in __libc_start_main () in /lib64/<a href="http://libc-2.12.so" target="_blank">libc-2.12.so</a><br>
> >> ><br>
> >> > This issue occurred on only RHEL 6.2, there is no problem on RHEL5.5.<br>
> >> > Now, I compiled WIEN2k with -static-libgc, which is one of options of Intel<br>
> >> > compiler, on RHEL5.5,<br>
> >> > I copied it to new server. ?Then, no error occurred.<br>
> >> ><br>
> >> > Although it may come from a problem of glibc of RHEL 6.2,<br>
> >> > had you had such a information, yet?<br>
> >> > If you know regarding this, please let me know anything.<br>
> >> ><br>
> >> > -----------------------------------------------------------------------<br>
> >> > I write our system informations :<br>
> >> ><br>
> >> > [The new system ]<br>
> >> > IBM BladeCenter HS22<br>
> >> > Operating System : Red Hat Enterprise Linux ComputeNode release 6.2<br>
> >> > (Santiago)<br>
> >> > CPU model : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz<br>
> >> > CPU cores : 12<br>
> >> > Memory : 24594924kB (free 14196424kB)<br>
> >> > Kernel : Linux 2.6.32-220.7.1.el6<br>
> >> > GLIBC : GNU C Library stable release version 2.12, by Roland McGrath et al.<br>
> >> ><br>
> >> > [RHEL 5.5 Systems]<br>
> >> > IBM iDataPlex dx360<br>
> >> > Operating System : Red Hat Enterprise Linux Server release 5.5 (Tikanga)<br>
> >> > CPU model : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz<br>
> >> > CPU cores : 12<br>
> >> > Memory : 24GB<br>
> >> > Kernel : Linux ?2.6.18-194.26.1.el5<br>
> >> > GLIBC : GNU C Library stable release version 2.5, by Roland McGrath et al.<br>
> >> ><br>
> >> > [Compiler]<br>
> >> > ifort version 12.1.0<br>
> >> > Intel(R) Math Kernel Library Version 10.3.6 Product Build 20110809 for<br>
> >> > Intel(R) 64 architecture applications<br>
> >> ><br>
> >> > [WIEN2k Compile options]<br>
> >> > WIEN2k version : WIEN2k_11.1<br>
> >> > FOPT:-free -mp1 -warn<br>
> >> > nogeneral -prec-div -pc80 -pad -ip -DINTEL_VML -traceback -g -openmp -static-libgcc<br>
> >> > current:LDFLAGS:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -static-libgcc<br>
> >> > DPARALLEL:'-DParallel'<br>
> >> > R_LIBS:$(MKLROOT)/lib/intel64/libmkl_blas95_lp64.a<br>
> >> > $(MKLROOT)/lib/intel64/libmkl_lapack95_lp64.a \<br>
> >> > -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a \<br>
> >> > $(MKLROOT)/lib/intel64/libmkl_intel_thread.a<br>
> >> > $(MKLROOT)/lib/intel64/libmkl_core.a \<br>
> >> > -Wl,--end-group -openmp -lpthread -lm<br>
> >> ><br>
> >> > * Not MPI version, but MKL + OpenMP version<br>
> >> ><br>
> >> > Thanks in advance.<br>
> >> > N.Igarashi<br>
> >> ><br>
> >> ><br>
> >> ><br>
> >> > _______________________________________________<br>
> >> > Wien mailing list<br>
> >> > <a href="mailto:Wien@zeus.theochem.tuwien.ac.at">Wien@zeus.theochem.tuwien.ac.at</a><br>
> >> > <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a><br>
> >><br>
> >><br>
> >><br>
> >> --<br>
> >> Professor Laurence Marks<br>
> >> Department of Materials Science and Engineering<br>
> >> Northwestern University<br>
> >> <a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a> 1-847-491-3996<br>
> >> "Research is to see what everybody else has seen, and to think what<br>
> >> nobody else has thought"<br>
> >> Albert Szent-Gyorgi<br>
> >> _______________________________________________<br>
> >> Wien mailing list<br>
> >> <a href="mailto:Wien@zeus.theochem.tuwien.ac.at">Wien@zeus.theochem.tuwien.ac.at</a><br>
> >> <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a><br>
> ><br>
> ><br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > Wien mailing list<br>
> > <a href="mailto:Wien@zeus.theochem.tuwien.ac.at">Wien@zeus.theochem.tuwien.ac.at</a><br>
> > <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a><br>
><br>
><br>
><br>
> --<br>
> Professor Laurence Marks<br>
> Department of Materials Science and Engineering<br>
> Northwestern University<br>
> <a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a> 1-847-491-3996<br>
> "Research is to see what everybody else has seen, and to think what<br>
> nobody else has thought"<br>
> Albert Szent-Gyorgi<br>
> _______________________________________________<br>
> Wien mailing list<br>
> <a href="mailto:Wien@zeus.theochem.tuwien.ac.at">Wien@zeus.theochem.tuwien.ac.at</a><br>
> <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a><br>
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</blockquote></div>