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
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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>
<tel:%2B1%20515-294-8971> (Office)
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"When you can do the common things of life in an uncommon
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<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> <http://vt.edu> | (540)
231-9080 <tel:%28540%29%20231-9080>
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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 <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
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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.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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