Nice catch on the readdir_r(). I wonder if the developers would appreciate a bug report and patch for your fix.
On Fri, Apr 22, 2011 at 1:05 PM, Ragothaman Yennamalli <[email protected]> wrote: > Hi all, > With the help of my colleague Nathan Weeks I am able to run pdb2gmx and all > other commands successfully . Here are his responses which he wanted me to > share with you in case someone is trying to install Gromacs in a similar > system. > > We set CFLAGS that way due to the following message when running configure: > > ######################################## > checking whether gcc-4.3.2 accepts -native -fast -xO5 -fsimple=2 > -fnonstd -dalign -O3 -fomit-frame-pointer -finline-functions -Wall > -Wno-unused -msse2 -funroll- > all-loops -std=gnu99... no > ******************************************************************* > * Sorry, these optimization settings don't seem to work for * > * your C compiler. Use make CFLAGS=..., or edit the top Makefile. * > ******************************************************************* > ######################################## > > The "-native -fast -xO5 -fsimple=2 -fnonstd -dalign" options that get > generated are for Solaris Studio, but we're using GCC. Also, > "-D_POSIX_PTHREAD_SEMANTICS" is required on Solaris to make use of the POSIX > versions of reentrant functions like ctime_r() and readdir_r() (if the > standard _POSIX_C_SOURCE or _XOPEN_SOURCE feature test macros > are set, _POSIX_PTHREAD_SEMANTICS will automatically be set as well). > > The memory fault that occurs when running pdb2gmx is due to a non-portable > use > of readdir_r() in futil.c; specifically, on Linux, the dirent structure > has a "char d_name[256]" member, and on Solaris, it is "char d_name[1]", and > the user is required to allocate memory to store its contents. The Linux > readdir(3) man page gives an example of how to do this portably: > > http://www.kernel.org/doc/man-pages/online/pages/man3/readdir.3.html > > I applied this method to futil.c, and it fixed the memory fault problem: > > ######################################## > --- src/gmxlib/futil.c.orig 2011-03-15 07:44:30.000000000 -0500 > +++ src/gmxlib/futil.c 2011-04-20 13:04:58.388912208 -0500 > @@ -37,6 +37,7 @@ > #include <config.h> > #endif > > +#include <stddef.h> > #include <stdio.h> > #include <stdlib.h> > #include <string.h> > @@ -595,22 +596,28 @@ > > #ifdef HAVE_DIRENT_H > > - struct dirent tmp_dirent; > + struct dirent * tmp_dirent; > struct dirent * p; > + size_t len; > > > if(gmxdir!=NULL && gmxdir->dirent_handle!=NULL) > { > - rc = readdir_r(gmxdir->dirent_handle,&tmp_dirent,&p); > + len = offsetof(struct dirent, d_name) > + + fpathconf(dirfd(gmxdir->dirent_handle), _PC_NAME_MAX) + 1; > + smalloc(tmp_dirent, len); > + rc = readdir_r(gmxdir->dirent_handle,tmp_dirent,&p); > + > if(p!=NULL && rc==0) > { > - strncpy(name,tmp_dirent.d_name,maxlength_name); > + strncpy(name,tmp_dirent->d_name,maxlength_name); > } > else > { > name[0] = '\0'; > rc = ENOENT; > } > + sfree(tmp_dirent); > } > else > { > ######################################## > >> Also why the make -j 48, when you only have 8 cores? > > We have 8 6-core CPUs (48 cores total). > >> I'm not even sure if the linker is ok with make -jN for building gromacs, >> it >> is not listed as compatible for *BSD ports. Also, does your make (I >> imagine >> this is Solaris make) have all the same semantics as gnu-make (gmake)? > > We are using GNU make. > >> And why did you switch your CC between fftw and gromacs configures? >> Solaris 'cc' may or may not be gcc43. Also, do we know if gcc43 is stable >> especially with -O3...Try removing -O3 or move it to -O2 at most... > > The Sun Studio 12.1 C compiler worked for fftw, but not for gromacs. > >> To rule out a bad fftw library, you can set --with-fft to use the builtin >> (slower) libfft instead of fftw (but fftw should not be affecting pdb2gmx >> I don't think...). >> >> I too have the questions of your CFLAGS, do you not require -m64 either? > > With gcc 4.3, there was a compilation error when -m64 was added to CFLAGS: > > ################################################### > make[5]: Entering directory > `/tmp//gromacs-4.5.4/src/gmxlib/nonbonded/nb_kernel_ia32_sse' > /bin/sh ../../../../libtool --mode=compile gcc-4.3.2 -m64 -g > -msse2 -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS -D_REENTRANT -pthread > -I./include -c -o nb_kernel010_ia32_sse.lo nb_kernel010_ia32_sse.s > gcc-4.3.2 -m64 -g -msse2 -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS > -D_REENTRANT -pthread -I./include -c nb_kernel010_ia32_sse.s -fPIC > -DPIC -o .libs/nb_kernel010_ia32_sse.o > nb_kernel010_ia32_sse.s: Assembler messages: > nb_kernel010_ia32_sse.s:87: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:89: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:90: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:91: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:92: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:93: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:94: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:795: Error: suffix or operands invalid for `pop' > nb_kernel010_ia32_sse.s:796: Error: suffix or operands invalid for `pop' > nb_kernel010_ia32_sse.s:797: Error: suffix or operands invalid for `pop' > nb_kernel010_ia32_sse.s:798: Error: suffix or operands invalid for `pop' > nb_kernel010_ia32_sse.s:799: Error: suffix or operands invalid for `pop' > nb_kernel010_ia32_sse.s:800: Error: suffix or operands invalid for `pop' > nb_kernel010_ia32_sse.s:865: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:867: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:868: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:869: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:870: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:871: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:872: Error: suffix or operands invalid for `push' > nb_kernel010_ia32_sse.s:1344: Error: suffix or operands invalid for `pop' > nb_kernel010_ia32_sse.s:1345: Error: suffix or operands invalid for `pop' > nb_kernel010_ia32_sse.s:1346: Error: suffix or operands invalid for `pop' > nb_kernel010_ia32_sse.s:1347: Error: suffix or operands invalid for `pop' > nb_kernel010_ia32_sse.s:1348: Error: suffix or operands invalid for `pop' > nb_kernel010_ia32_sse.s:1349: Error: suffix or operands invalid for `pop' > make[5]: *** [nb_kernel010_ia32_sse.lo] Error 1 > ############################################## > > > -- > **************************************** > Ragothaman M Yennamalli, Ph.D. > Postdoctoral Research Associate > 1012 Crop Genome Informatics Laboratory > Department of Genetics, Development and Cell Biology > Iowa State University > Ames, Iowa 50011-3260 USA > > +1 515-294-8971 (Office) > +1 515-294-8280 (Fax) > +1 515-851-1016 (Mobile) > > "When you can do the common things of life in an uncommon way, you will > command the attention of the world." -George Washington Carver > > http://www.public.iastate.edu/~raghu/ > http://www.artistrkrishnarao.com/ > > *************************************** > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
