Dear Justin, I am having grompp segmentation error only for the drug-enzyme complex tutorial, all other executables are ok, can this occur due to the any other reasons like following the tutorial improperly.
Thanks, Ram On Tue, Jan 5, 2010 at 1:24 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks for the response. >> >> Here is the info regarding the cluster where gromacs version 4.0.5 is >> installed with icc compliers. >> >> $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2 >> uname -m = x86_64 >> uname -r = 2.6.18-128.7.1.el5 >> uname -s = Linux >> uname -v = #1 SMP Mon Aug 24 08:21:56 EDT 2009 >> compilers: C and fortran Intel 10.1 >> >> Please suggest me as the grompp command also donot work with this >> configuration. > > Does grompp give any other output, or does it just seg fault? Do other > executables work on this system? > > There are a whole host of issues that could be causing this, from 32/64 bit > mismatch, shared libraries being moved, etc, so it is very difficult to > diagnose. Was the whole package compiled with MPI (per the above command)? > If so, there is no point, since the only MPI-enabled executable is mdrun. > It may help to re-compile correctly if this is the case (a bit of a long > shot, but perhaps worth trying). Do you have gcc available on the cluster, > to test and see if it produces functioning code? > > -Justin > >> >> Thanks, >> >> Ram >> >> On Mon, Jan 4, 2010 at 6:17 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> ram bio wrote: >>>> >>>> Dear Justin, >>>> >>>> Thanks for the response. >>>> >>>> I am using gromacs 4.0.3 version on my PC and 4.0.5 on cluster, I have >>>> asked my system admin to provide the details regarding the cluster, >>>> whereas for my PC: >>>> >>>> The info is as follows: >>>> >>>> 1. The Gromacs version you are using. - 4.0.3 >>>> 2. The compilers used in installing Gromacs.- gcc >>>> gcc -v >>>> Using built-in specs. >>>> Target: i386-redhat-linux >>>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man >>>> --infodir=/usr/share/info --enable-shared --enable-threads=posix >>>> --enable-checking=release --with-system-zlib --enable-__cxa_atexit >>>> --disable-libunwind-exceptions --enable-libgcj-multifile >>>> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada >>>> --enable-java-awt=gtk --disable-dssi --enable-plugin >>>> --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre >>>> --with-cpu=generic --host=i386-redhat-linux >>>> Thread model: posix >>>> gcc version 4.1.2 20080704 (Red Hat 4.1.2-44) >>>> >>> The gcc 4.1.x is well-known to be buggy, and as advised on the Gromacs >>> source code download site: >>> >>> "WARNING: do not use the gcc 4.1.x set of compilers. They are broken. >>> These >>> compilers come with recent Linux distrubutions like Fedora 5/6 etc." >>> >>> I would suggest updating to the latest version of Gromacs (4.0.7), using >>> a >>> more reliable compiler (other versions of gcc, i.e. 4.0.x and older, and >>> 4.2.x and newer, are fine). >>> >>>> 3. Options specified during configuration. >>>> >>>> I didnot get this, can you please elaborate... >>>> >>> Things like --enable-shared, --disable-(whatever), but I don't know that >>> any >>> of this is relevant. I think the compiler is the problem. >>> >>> -Justin >>> >>>> 4. Specifications of your hardware. >>>> >>>> processor : 0 >>>> vendor_id : GenuineIntel >>>> cpu family : 6 >>>> model : 13 >>>> model name : Intel(R) Pentium(R) M processor 1.70GHz >>>> stepping : 6 >>>> cpu MHz : 600.000 >>>> cache size : 2048 KB >>>> fdiv_bug : no >>>> hlt_bug : no >>>> f00f_bug : no >>>> coma_bug : no >>>> fpu : yes >>>> fpu_exception : yes >>>> cpuid level : 2 >>>> wp : yes >>>> flags : fpu vme de pse tsc msr mce cx8 mtrr pge mca cmov pat >>>> clflush dts acpi mmx fxsr sse sse2 ss tm pbe up est tm2 >>>> bogomips : 1196.53 >>>> >>>> Linux version 2.6.18-8.el5 (mockbu...@builder4.centos.org) (gcc >>>> version 4.1.1 20070105 (Red Hat 4.1.1-52)) #1 SMP Thu Mar 15 19:57:35 >>>> EDT 2007 >>>> >>>> Build Operating System: Linux 2.6.18-53.1.14.el5PAE i686 Red Hat, Inc. >>>> Current Operating System: Linux localhost.localdomain 2.6.18-8.el5 #1 >>>> SMP Thu Mar 15 19:57:35 EDT 2007 i686 >>>> Build Date: 21 June 2008 >>>> Build ID: xorg-x11-server 1.1.1-48.41.el5_2.1 >>>> >>>> >>>> I would be providing the info about the cluster, once I receive it, >>>> mean please let me know if any info is missing and help me. >>>> >>>> Thanks, >>>> >>>> Ram >>>> >>>> >>>> >>>> >>>> >>>> On Thu, Dec 31, 2009 at 11:49 PM, Justin A. Lemkul <jalem...@vt.edu> >>>> wrote: >>>>> >>>>> ram bio wrote: >>>>>> >>>>>> Dear Gromacs Users, >>>>>> >>>>>> Iam following Drug/Enzyme complex solvation tutorial by John E. >>>>>> Kerrigan, I am unable to execute the grompp step as per the tutorial, >>>>>> the output of grompp command is as follows: >>>>>> >>>>>> grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr >>>>>> >>>>>> >>>>>> :-) grompp (-: >>>>>> >>>>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# >>>>>> checking input for internal consistency... >>>>>> processing topology... >>>>>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp >>>>>> Opening library file >>>>>> /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp >>>>>> Opening library file >>>>>> /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp >>>>>> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp >>>>>> Segmentation fault >>>>>> >>>>>> what i have done is as per the tutorial, that is >>>>>> 1) generated the drg.itp using prodrug beta >>>>>> 2) executed pdb2gmx using 4 that is ff53a6 ff >>>>>> 3) edit the drg.itp by removing the lines redundant as per trp.top >>>>>> 4) edit trp.gro by adding drg coordinates and chainging the numbers >>>>>> >>>>>> please help me to overcome this error, for your convenience I have >>>>>> attached the drg.itp, trp.top, trp.gro and trp_b4ion.gro files. >>>>>> >>>>> I doubt any of these files will be useful. Better information would >>>>> include: >>>>> >>>>> 1. The Gromacs version you are using. >>>>> 2. The compilers used in installing Gromacs. >>>>> 3. Options specified during configuration. >>>>> 4. Specifications of your hardware. >>>>> >>>>> A segmentation fault is a memory error and can have numerous causes. >>>>> The >>>>> above information may be useful. >>>>> >>>>> -Justin >>>>> >>>>>> Thanks, >>>>>> >>>>>> Ram >>>>>> 4 attachments — >>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> Justin A. Lemkul >>>>> Ph.D. Candidate >>>>> ICTAS Doctoral Scholar >>>>> MILES-IGERT Trainee >>>>> Department of Biochemistry >>>>> Virginia Tech >>>>> Blacksburg, VA >>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>>> >>>>> ======================================== >>>>> -- >>>>> gmx-users mailing list gmx-us...@gromacs.org >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/search before >>>>> posting! >>>>> Please don't post (un)subscribe requests to the list. Use the www >>>>> interface >>>>> or send it to gmx-users-requ...@gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-us...@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? 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