Re: [gmx-users] pdb2gmx segmentation fault
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 07:44:30.0 -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
Re: [gmx-users] pdb2gmx segmentation fault
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
ragotha...@gmail.com 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 07:44:30.0 -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
Re: [gmx-users] pdb2gmx segmentation fault
Matthew Zwier wrote:
Nice catch on the readdir_r(). I wonder if the developers would
appreciate a bug report and patch for your fix.
Yes, please file an issue report on redmine.gromacs.org. If it doesn't get put
on a to-do list, it probably won't get done :)
-Justin
On Fri, Apr 22, 2011 at 1:05 PM, Ragothaman Yennamalli
ragotha...@gmail.com 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 07:44:30.0 -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
Re: [gmx-users] pdb2gmx segmentation fault
Thanks for the link. Have just filed it. Thanks and Regards, Raghu On Fri, Apr 22, 2011 at 1:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: Matthew Zwier wrote: Nice catch on the readdir_r(). I wonder if the developers would appreciate a bug report and patch for your fix. Yes, please file an issue report on redmine.gromacs.org. If it doesn't get put on a to-do list, it probably won't get done :) -Justin -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. Mark -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org mailto: gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au mailto: 4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. Mark -- 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.public.iastate.edu/%7Eraghu/ http://www.artistrkrishnarao.com/ *** -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
Ragothaman Yennamalli wrote: These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' I'm no compiler expert, but is it necessary to set all these CFLAGS here? Does the installation fail for some reason if they're not set? Also, how is Gromacs finding FFTW? You haven't set the CPPFLAGS or LDFLAGS. make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. This would indicate to me that the problem is not necessarily in Gromacs, but the way you're installing it, and as Mark suggested, is probably related to some static/shared library issue. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. Mark -- 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 tel:%2B1%20515-294-8971 (Office) +1 515-294-8280 tel:%2B1%20515-294-8280 (Fax) +1 515-851-1016 tel:%2B1%20515-851-1016 (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.public.iastate.edu/%7Eraghu/ http://www.public.iastate.edu/%7Eraghu/ http://www.artistrkrishnarao.com/ *** -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department
Re: [gmx-users] pdb2gmx segmentation fault
Dear Justin, Thanks for the mail. Yes, without these CFLAGS the make was not successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring gromacs. Since without it it would have stopped compiling. I want to agree with you that it is some issue with shared libraries, but i dont think it is the issue since I have used the flag --enable-shared. Also, if this was the case then editconf would not have worked as well. Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' I'm no compiler expert, but is it necessary to set all these CFLAGS here? Does the installation fail for some reason if they're not set? Also, how is Gromacs finding FFTW? You haven't set the CPPFLAGS or LDFLAGS. make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. This would indicate to me that the problem is not necessarily in Gromacs, but the way you're installing it, and as Mark suggested, is probably related to some static/shared library issue. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. Mark -- 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 tel:%2B1%20515-294-8971 (Office) +1 515-294-8280 tel:%2B1%20515-294-8280 (Fax) +1 515-851-1016 tel:%2B1%20515-851-1016 (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.public.iastate.edu/%7Eraghu/ http://www.public.iastate.edu/%7Eraghu/ http://www.artistrkrishnarao.com/ *** -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org
Re: [gmx-users] pdb2gmx segmentation fault
Ragothaman Yennamalli wrote: Dear Justin, Thanks for the mail. Yes, without these CFLAGS the make was not successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring gromacs. Since without it it would have stopped compiling. I want to agree with you that it is some issue with shared libraries, but i dont think it is the issue since I have used the flag --enable-shared. Also, You did --enable-shared for FFTW, but not Gromacs. Perhaps there is some mismatch there. if this was the case then editconf would not have worked as well. I wouldn't rule it out just yet. If the installation was successful, everything would work. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' I'm no compiler expert, but is it necessary to set all these CFLAGS here? Does the installation fail for some reason if they're not set? Also, how is Gromacs finding FFTW? You haven't set the CPPFLAGS or LDFLAGS. make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. This would indicate to me that the problem is not necessarily in Gromacs, but the way you're installing it, and as Mark suggested, is probably related to some static/shared library issue. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. Mark -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department of Genetics
Re: [gmx-users] pdb2gmx segmentation fault
On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: Dear Justin, Thanks for the mail. Yes, without these CFLAGS the make was not successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring gromacs. Since without it it would have stopped compiling. I want to agree with you that it is some issue with shared libraries, but i dont think it is the issue since I have used the flag --enable-shared. Also, You did --enable-shared for FFTW, but not Gromacs. Perhaps there is some mismatch there. Since configure did not have any such option, i did not use it. However, I tried compiling with --enable-shared to reinstall gromacs. It installed without any issues. But, the same segmentation fault. if this was the case then editconf would not have worked as well. I wouldn't rule it out just yet. If the installation was successful, everything would work. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' I'm no compiler expert, but is it necessary to set all these CFLAGS here? Does the installation fail for some reason if they're not set? Also, how is Gromacs finding FFTW? You haven't set the CPPFLAGS or LDFLAGS. make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. This would indicate to me that the problem is not necessarily in Gromacs, but the way you're installing it, and as Mark suggested, is probably related to some static/shared library issue. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new
Re: [gmx-users] pdb2gmx segmentation fault
I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused you to need to define that flag? Also...what hardware (cpu) and operating system (linux? what distro? what version?) are you using? Matt Z. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs. On Wed, Apr 20, 2011 at 11:34 AM, Matthew Zwier mczw...@gmail.com wrote: I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused you to need to define that flag? Also...what hardware (cpu) and operating system (linux? what distro? what version?) are you using? Matt Z. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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.gromacs.org/Support/Mailing_Lists http://www.public.iastate.edu/~raghu/ http://www.artistrkrishnarao.com/ *** -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
Thanks. I'm no Sun expert, so I'd have to echo Justin's request for the precise sequence of commands you used to install GROMACS and all dependencies. On Wed, Apr 20, 2011 at 2:51 PM, Ragothaman Yennamalli ragotha...@gmail.com wrote: It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs. On Wed, Apr 20, 2011 at 11:34 AM, Matthew Zwier mczw...@gmail.com wrote: I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused you to need to define that flag? Also...what hardware (cpu) and operating system (linux? what distro? what version?) are you using? Matt Z. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
Matthew Zwier wrote: Thanks. I'm no Sun expert, so I'd have to echo Justin's request for the precise sequence of commands you used to install GROMACS and all dependencies. In addition, you can add -g to your CFLAGS to get debugging symbols, then execute pdb2gmx via a debugger like gdb. This should show where the problem is coming from. I have also never used Sun, so I won't be able to comment directly on that, either. -Justin On Wed, Apr 20, 2011 at 2:51 PM, Ragothaman Yennamalli ragotha...@gmail.com wrote: It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs. On Wed, Apr 20, 2011 at 11:34 AM, Matthew Zwier mczw...@gmail.com wrote: I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused you to need to define that flag? Also...what hardware (cpu) and operating system (linux? what distro? what version?) are you using? Matt Z. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
Also why the make -j 48, when you only have 8 cores? 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)? 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... 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? On 2011-04-20 10:23:25AM -0500, Ragothaman Yennamalli wrote: On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: Dear Justin, Thanks for the mail. Yes, without these CFLAGS the make was not successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring gromacs. Since without it it would have stopped compiling. I want to agree with you that it is some issue with shared libraries, but i dont think it is the issue since I have used the flag --enable-shared. Also, You did --enable-shared for FFTW, but not Gromacs. Perhaps there is some mismatch there. Since configure did not have any such option, i did not use it. However, I tried compiling with --enable-shared to reinstall gromacs. It installed without any issues. But, the same segmentation fault. if this was the case then editconf would not have worked as well. I wouldn't rule it out just yet. If the installation was successful, everything would work. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu mailto:jalem...@vt.edumailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' I'm no compiler expert, but is it necessary to set all these CFLAGS here? Does the installation fail for some reason if they're not set? Also, how is Gromacs finding FFTW? You haven't set the CPPFLAGS or LDFLAGS. make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. This would indicate to me that the problem is not necessarily in Gromacs, but the way you're installing it, and as Mark suggested, is probably related to some static/shared library issue. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu mailto:jalem...@vt.edumailto:jalem...@vt.edu mailto:jalem...@vt.edumailto:jalem...@vt.edu mailto:jalem...@vt.edumailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org
[gmx-users] pdb2gmx segmentation fault
Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Please let me know what am I missing. Thanks and Regards, Raghu -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx: segmentation fault
Hi Tsjerk, Ya, it happened with other ff, too. My command line is pdb2gmx -ignh -f Sur.pdb i've browsed through the pdb file and it looks ok... joyce From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, January 13, 2011 15:31:35 Subject: Re: [gmx-users] pdb2gmx: segmentation fault Hi Joyce, Can you post the command line? Does it also happen with other force fields? Is there something notable about the pdb file? Cheers, Tsjerk On Jan 13, 2011 7:48 AM, Kwee Hong jestan1...@yahoo.com wrote: Hi Mark, I tried v 4.0.7 and 4.5.1. Both experiencing the same situation. The file is actually saved as pdb file from autodock output using pymol. Joyce From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, January 13, 2011 13:43:47 Subject: Re: [gmx-users] pdb2gmx: segmentation fault On 01/13/11, Kwee Hong jestan1...@yahoo.com wrote: Hi,I was trying to generate topolo... -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pdb2gmx: segmentation fault
Hi, I was trying to generate topology file of my pdb using pdb2gmx. Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 4 Opening library file /usr/share/gromacs/top/ffG53a6.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading complex_SurA.pdb... Read 3163 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 409 residues with 3163 atoms chain #res #atoms 1 'B' 409 3163 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffG53a6.atp Atomtype 1 Reading residue database... (ffG53a6) Opening library file /usr/share/gromacs/top/ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening library file /usr/share/gromacs/top/ffG53a6.hdb Opening library file /usr/share/gromacs/top/ffG53a6-n.tdb Opening library file /usr/share/gromacs/top/ffG53a6-c.tdb Back Off! I just backed up topol_SurA.top to ./#topol_SurA.top.1# Processing chain 1 'B' (3163 atoms, 409 residues) There are 629 donors and 614 acceptors Segmentation fault Yet I encountered segmentation fault which I don't understand why this happen. All suggestion are welcomed? Thanks. Joyce -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx: segmentation fault
On 01/13/11, Kwee Hong jestan1...@yahoo.com wrote:
!-- DIV {margin:0px;} --
Hi,
I was trying to generate topology file of my pdb using pdb2gmx.
Select the Force Field:
0: GROMOS96 43a1 force
field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED]
Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum charges
9: Encad all-atom force field, using full solvent charges
4
Opening library file /usr/share/gromacs/top/ffG53a6.rtp
Opening library file
/usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/share/gromacs/top/electroneg.dat
Entries
in electroneg.dat: 71
Opening library file /usr/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading complex_SurA.pdb...
Read 3163 atoms
Opening library file /usr/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 409 residues with 3163 atoms
chain #res #atoms
1 'B' 409 3163
All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /usr/share/gromacs/top/ffG53a6.atp
Atomtype 1
Reading residue database... (ffG53a6)
Opening library file /usr/share/gromacs/top/ffG53a6.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing impropers on same bond as a proper
Residue 108
Sorting it all out...
Opening library file /usr/share/gromacs/top/ffG53a6.hdb
Opening library file /usr/share/gromacs/top/ffG53a6-n.tdb
Opening library file /usr/share/gromacs/top/ffG53a6-c.tdb
Back Off! I just backed up topol_SurA.top to ./#topol_SurA.top.1#
Processing chain 1 'B' (3163 atoms, 409 residues)
There are 629 donors and 614 acceptors
Segmentation fault
Yet I encountered segmentation fault which I don't understand why this happen.
All suggestion are welcomed?
Please remember to announce your GROMACS version when discussing problems, and
to try the latest one.
Mark
--
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Re: [gmx-users] pdb2gmx: segmentation fault
Hi Mark, I tried v 4.0.7 and 4.5.1. Both experiencing the same situation. The file is actually saved as pdb file from autodock output using pymol. Joyce From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, January 13, 2011 13:43:47 Subject: Re: [gmx-users] pdb2gmx: segmentation fault On 01/13/11, Kwee Hong jestan1...@yahoo.com wrote: Hi, I was trying to generate topology file of my pdb using pdb2gmx. Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 4 Opening library file /usr/share/gromacs/top/ffG53a6.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading complex_SurA.pdb... Read 3163 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 409 residues with 3163 atoms chain #res #atoms 1 'B' 409 3163 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffG53a6.atp Atomtype 1 Reading residue database... (ffG53a6) Opening library file /usr/share/gromacs/top/ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening library file /usr/share/gromacs/top/ffG53a6.hdb Opening library file /usr/share/gromacs/top/ffG53a6-n.tdb Opening library file /usr/share/gromacs/top/ffG53a6-c.tdb Back Off! I just backed up topol_SurA.top to ./#topol_SurA.top.1# Processing chain 1 'B' (3163 atoms, 409 residues) There are 629 donors and 614 acceptors Segmentation fault Yet I encountered segmentation fault which I don't understand why this happen. All suggestion are welcomed? Please remember to announce your GROMACS version when discussing problems, and to try the latest one. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx: segmentation fault
Hi Joyce, Can you post the command line? Does it also happen with other force fields? Is there something notable about the pdb file? Cheers, Tsjerk On Jan 13, 2011 7:48 AM, Kwee Hong jestan1...@yahoo.com wrote: Hi Mark, I tried v 4.0.7 and 4.5.1. Both experiencing the same situation. The file is actually saved as pdb file from autodock output using pymol. Joyce -- *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, January 13, 2011 13:43:47 *Subject:* Re: [gmx-users] pdb2gmx: segmentation fault On 01/13/11, Kwee Hong jestan1...@yahoo.com wrote: Hi,I was trying to generate topolo... -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
