Re: [gmx-users] pdb2gmx segmentation fault

[Ragothaman Yennamalli]

Thanks for the link. Have just filed it.
Thanks and Regards,
Raghu

On Fri, Apr 22, 2011 at 1:12 PM, Justin A. Lemkul  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/

***
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Re: [gmx-users] pdb2gmx segmentation fault

[Justin A. Lemkul]

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
 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 
 #endif

+#include 
 #include 
 #include 
 #include 
@@ -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_

Re: [gmx-users] pdb2gmx segmentation fault

[Matthew Zwier]

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
 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 
>  #endif
>
> +#include 
>  #include 
>  #include 
>  #include 
> @@ -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: E

Re: [gmx-users] pdb2gmx segmentation fault

[Ragothaman Yennamalli]

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 
 #endif

+#include 
 #include 
 #include 
 #include 
@@ -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 operan

Re: [gmx-users] pdb2gmx segmentation fault

[Peter C. Lai]

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 
> mailto: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 
> mailto:jalem...@vt.edu> 
> <mailto: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
>mailto:jalem...@vt.edu> 
> <mailto:jalem...@vt.edu<mailto:jalem...@vt.edu>>
><mailto: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,
>   Rag

Re: [gmx-users] pdb2gmx segmentation fault

[Justin A. Lemkul]

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
 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  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.
--
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--

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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Please search the archive at
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--


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


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Re: [gmx-users] pdb2gmx segmentation fault

[Matthew Zwier]

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
 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  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
>
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Re: [gmx-users] pdb2gmx segmentation fault

[Ragothaman Yennamalli]

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  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/
>
> ***
>
>
>
>
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Please search the archive at 
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Re: [gmx-users] pdb2gmx segmentation fault

[Matthew Zwier]

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!
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Re: [gmx-users] pdb2gmx segmentation fault

[Ragothaman Yennamalli]

On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul  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.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
>>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
>>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

Re: [gmx-users] pdb2gmx segmentation fault

[Justin A. Lemkul]

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 <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
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
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




   -- 
 

Re: [gmx-users] pdb2gmx segmentation fault

[Ragothaman Yennamalli]

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  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>> 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 ><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  (Office)
>>+1 515-294-8280  (Fax)
>>+1 515-851-1016  (Mobile)
>>
>>
>>"When you can do the common things of life in an uncommon

Re: [gmx-users] pdb2gmx segmentation fault

[Justin A. Lemkul]

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 <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 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  (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.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

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

Re: [gmx-users] pdb2gmx segmentation fault

[Ragothaman Yennamalli]

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  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>>
>> Message-ID: <4dae452b.3090...@anu.edu.au > 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/

***
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Re: [gmx-users] pdb2gmx segmentation fault

[Justin A. Lemkul]

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 <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


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Re: [gmx-users] pdb2gmx segmentation fault

[Ragothaman Yennamalli]

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 
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/

***
-- 
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Re: [gmx-users] pdb2gmx segmentation fault

[Mark Abraham]

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



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[gmx-users] pdb2gmx segmentation fault

[Ragothaman Yennamalli]

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
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Re: [gmx-users] pdb2gmx: segmentation fault

[Kwee Hong]

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 
To: Discussion list for GROMACS users 
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"  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 
>To: Discussion list for GROMACS users 
>Sent: Thursday, January 13, 2011 13:43:47
>Subject: Re: [gmx-users] pdb2gmx: segmentation  fault
>
>On 01/13/11, Kwee Hong  wrote: > > Hi, > >  I was trying 
>to generate topolo...
>
>--
>gmx-users mailing listgmx-users@gromacs.org
>http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] pdb2gmx: segmentation fault

[Tsjerk Wassenaar]

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"  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 
*To:* Discussion list for GROMACS users 
*Sent:* Thursday, January 13, 2011 13:43:47
*Subject:* Re: [gmx-users] pdb2gmx: segmentation fault

On 01/13/11, Kwee Hong  wrote: > > Hi, > >  I was
trying to generate topolo...


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Re: [gmx-users] pdb2gmx: segmentation fault

[Kwee Hong]

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 
To: Discussion list for GROMACS users 
Sent: Thursday, January 13, 2011 13:43:47
Subject: Re: [gmx-users] pdb2gmx: segmentation fault



On 01/13/11, Kwee Hong   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


> 

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Re: [gmx-users] pdb2gmx: segmentation fault

[Mark Abraham]

On 01/13/11, Kwee Hong   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

> 
> 
> 
> 
> 
> 
> 
>
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[gmx-users] pdb2gmx: segmentation fault

[Kwee Hong]

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


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