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/ ***************************************
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