On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul <[email protected]> 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 <[email protected]<mailto: >> [email protected]>> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> <mailto:[email protected] >> >> <mailto:[email protected]> >> >> <mailto:[email protected] >> <mailto:[email protected]>>>> >> Message-ID: <[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>> >> >> 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> >> <tel:%2B1%20515-294-8971> (Office) >> +1 515-294-8280 <tel:%2B1%20515-294-8280> >> <tel:%2B1%20515-294-8280> (Fax) >> +1 515-851-1016 <tel:%2B1%20515-851-1016> >> <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.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> >> <tel:%28540%29%20231-9080> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> 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 [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> >> 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 <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 list [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> 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.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 [email protected] > 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 [email protected]. > 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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