Re: [gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon "Woodcrest"
Hi, This bug is now fixed in git release-4-5-patches (commit 0a31a047f429). Rossen On 8/6/10 11:33 AM, david.groc...@uk.fujitsu.com wrote: Hi, this is the first time I have messaged this group, so please bear with me. I have had little trouble with previous versions (4.0.7 for example), however with this version the pdb2gmx program gives a segmentation fault error if run stand-alone, even with no input. When compiled with debug, idb claims it is a "strlen" problem in glibc. Running either grompp or mdrun or any other of the executables without any input files merely yields the help screen (as expected). The single precision version works fine with Intel Compiler and MKL ! The double precision version works with GNU compiler and MKL, but I need it to work with Intel When compiling the double precision version 4.0.7, I found that I needed to use the configure option --disable-x86-64-sse For 4.5b2, I have downloaded both the current version from Git (05Aug - 1500 BST), as well as the tar.gz versions and got the same problem. I compiled with icc 10.1 and am using mkl 10.2 on very standard Linux distribution. Here is my configure line ./configure CC=icc CPPFLAGS="-I$MKL_ROOT/include" LDFLAGS="-L$MKL_ROOT/lib/" --with-fft=mkl --prefix=$HOME/gromacs-4.5b2/icc/double --enable-double --program-suffix=""LD=icc Followed by "make -j 4&& make install" Has anyone else tried this yet ? It seems like a quite trivial bug. Thanks David David Grocutt Environment& Health Research Division Fujitsu Laboratories of Europe Phone: +44 (0) 208 606 4533 Fax: +44 (0) 208 606 4539 Email david.groc...@uk.fujitsu.com __ Fujitsu Laboratories of Europe Limited Hayes Park Central, Hayes End Road, Hayes, Middlesex, UB4 8FE Registered No. 4153469 This e-mail and any attachments are for the sole use of addressee(s) and may contain information which is privileged and confidential. Unauthorised use or copying for disclosure is strictly prohibited. The fact that this e-mail has been scanned by Trendmicro Interscan does not guarantee that it has not been intercepted or amended nor that it is virus-free. -- gmx-users mailing listgmx-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? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon "Woodcrest"
- Original Message - From: david.groc...@uk.fujitsu.com Date: Tuesday, August 10, 2010 1:25 Subject: [gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon "Woodcrest" To: gmx-users@gromacs.org > Hi, this is the first time I have messaged this group, so please > bear with me. > > I have had little trouble with previous versions (4.0.7 for > example), however with this version the pdb2gmx program gives a > segmentation fault error if run stand-alone, even with no input. > When compiled with debug, idb claims it is a "strlen" problem in > glibc. Running either grompp or mdrun or any other of the > executables without any input files merely yields the help > screen (as expected). > > The single precision version works fine with Intel Compiler and > MKL ! > The double precision version works with GNU compiler and MKL, > but I need it to work with Intel Not really. icc+MKL provides a miniscule improvement over gcc+FFTW3, so if the former gives trouble, use the latter. Search the archive, I probably published some 4.0.7 numbers. > When compiling the double precision version 4.0.7, I found that > I needed to use the configure option --disable-x86-64-sse That is probably to be expected. If these Woodcrest processors are in some Altix machine, then there's a history of unresolved problems with these nonbonded kernels on such machines. The problem seems not to be with the kernels. Search the archives if relevant. > For 4.5b2, I have downloaded both the current version from Git > (05Aug - 1500 BST), as well as the tar.gz versions and got the > same problem. > > I compiled with icc 10.1 and am using mkl 10.2 on very standard > Linux distribution. > > Here is my configure line > > ./configure CC=icc CPPFLAGS="-I$MKL_ROOT/include" LDFLAGS="- > L$MKL_ROOT/lib/" --with-fft=mkl --prefix=$HOME/gromacs- > 4.5b2/icc/double --enable-double --program- > suffix=""LD=icc Something's gotten mangled here - the line's incomplete. One needs to take particular care to link correctly to MKL - consult the MKL docs for your system. > Followed by "make -j 4 && make install" > > Has anyone else tried this yet ? It seems like a quite trivial bug. icc 11.1 + mkl + double works fine on my Intel Nehalem machine. Mark -- gmx-users mailing listgmx-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? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon "Woodcrest"
Hi, this is the first time I have messaged this group, so please bear with me. I have had little trouble with previous versions (4.0.7 for example), however with this version the pdb2gmx program gives a segmentation fault error if run stand-alone, even with no input. When compiled with debug, idb claims it is a "strlen" problem in glibc. Running either grompp or mdrun or any other of the executables without any input files merely yields the help screen (as expected). The single precision version works fine with Intel Compiler and MKL ! The double precision version works with GNU compiler and MKL, but I need it to work with Intel When compiling the double precision version 4.0.7, I found that I needed to use the configure option --disable-x86-64-sse For 4.5b2, I have downloaded both the current version from Git (05Aug - 1500 BST), as well as the tar.gz versions and got the same problem. I compiled with icc 10.1 and am using mkl 10.2 on very standard Linux distribution. Here is my configure line ./configure CC=icc CPPFLAGS="-I$MKL_ROOT/include" LDFLAGS="-L$MKL_ROOT/lib/" --with-fft=mkl --prefix=$HOME/gromacs-4.5b2/icc/double --enable-double --program-suffix=""LD=icc Followed by "make -j 4 && make install" Has anyone else tried this yet ? It seems like a quite trivial bug. Thanks David __ Fujitsu Laboratories of Europe Limited Hayes Park Central, Hayes End Road, Hayes, Middlesex, UB4 8FE Registered No. 4153469 This e-mail and any attachments are for the sole use of addressee(s) and may contain information which is privileged and confidential. Unauthorised use or copying for disclosure is strictly prohibited. The fact that this e-mail has been scanned by Trendmicro Interscan does not guarantee that it has not been intercepted or amended nor that it is virus-free. -- gmx-users mailing listgmx-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? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon "Woodcrest"
Hi, I can reproduce it. Probably won't have time till Monday to look at the reason. Roland On Fri, Aug 6, 2010 at 5:33 AM, wrote: > Hi, this is the first time I have messaged this group, so please bear with > me. > > I have had little trouble with previous versions (4.0.7 for example), > however with this version the pdb2gmx program gives a segmentation fault > error if run stand-alone, even with no input. When compiled with debug, idb > claims it is a "strlen" problem in glibc. Running either grompp or mdrun or > any other of the executables without any input files merely yields the help > screen (as expected). > > The single precision version works fine with Intel Compiler and MKL ! > The double precision version works with GNU compiler and MKL, but I need it > to work with Intel > > When compiling the double precision version 4.0.7, I found that I needed to > use the configure option --disable-x86-64-sse > > > For 4.5b2, I have downloaded both the current version from Git (05Aug - > 1500 BST), as well as the tar.gz versions and got the same problem. > > I compiled with icc 10.1 and am using mkl 10.2 on very standard Linux > distribution. > > Here is my configure line > > ./configure CC=icc CPPFLAGS="-I$MKL_ROOT/include" > LDFLAGS="-L$MKL_ROOT/lib/" --with-fft=mkl > --prefix=$HOME/gromacs-4.5b2/icc/double --enable-double > --program-suffix=""LD=icc > > Followed by "make -j 4 && make install" > > Has anyone else tried this yet ? It seems like a quite trivial bug. > > Thanks > > David > > David Grocutt > Environment & Health Research Division > Fujitsu Laboratories of Europe > Phone: +44 (0) 208 606 4533 > Fax: +44 (0) 208 606 4539 > Email david.groc...@uk.fujitsu.com > > > __ > > Fujitsu Laboratories of Europe Limited > Hayes Park Central, Hayes End Road, Hayes, Middlesex, UB4 8FE > Registered No. 4153469 > > This e-mail and any attachments are for the sole use of addressee(s) and > may contain information which is privileged and confidential. Unauthorised > use or copying for disclosure is strictly prohibited. The fact that this > e-mail has been scanned by Trendmicro Interscan does not guarantee that > it has not been intercepted or amended nor that it is virus-free. > > -- > gmx-users mailing listgmx-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? Read http://www.gromacs.org/mailing_lists/users.php > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-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? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon "Woodcrest"
Hi, this is the first time I have messaged this group, so please bear with me. I have had little trouble with previous versions (4.0.7 for example), however with this version the pdb2gmx program gives a segmentation fault error if run stand-alone, even with no input. When compiled with debug, idb claims it is a "strlen" problem in glibc. Running either grompp or mdrun or any other of the executables without any input files merely yields the help screen (as expected). The single precision version works fine with Intel Compiler and MKL ! The double precision version works with GNU compiler and MKL, but I need it to work with Intel When compiling the double precision version 4.0.7, I found that I needed to use the configure option --disable-x86-64-sse For 4.5b2, I have downloaded both the current version from Git (05Aug - 1500 BST), as well as the tar.gz versions and got the same problem. I compiled with icc 10.1 and am using mkl 10.2 on very standard Linux distribution. Here is my configure line ./configure CC=icc CPPFLAGS="-I$MKL_ROOT/include" LDFLAGS="-L$MKL_ROOT/lib/" --with-fft=mkl --prefix=$HOME/gromacs-4.5b2/icc/double --enable-double --program-suffix=""LD=icc Followed by "make -j 4 && make install" Has anyone else tried this yet ? It seems like a quite trivial bug. Thanks David David Grocutt Environment & Health Research Division Fujitsu Laboratories of Europe Phone: +44 (0) 208 606 4533 Fax: +44 (0) 208 606 4539 Email david.groc...@uk.fujitsu.com __ Fujitsu Laboratories of Europe Limited Hayes Park Central, Hayes End Road, Hayes, Middlesex, UB4 8FE Registered No. 4153469 This e-mail and any attachments are for the sole use of addressee(s) and may contain information which is privileged and confidential. Unauthorised use or copying for disclosure is strictly prohibited. The fact that this e-mail has been scanned by Trendmicro Interscan does not guarantee that it has not been intercepted or amended nor that it is virus-free. -- gmx-users mailing listgmx-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? Read http://www.gromacs.org/mailing_lists/users.php
