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