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Cannot Compute Sizeof Int Gromacs

Use the www interface or send it to [EMAIL PROTECTED] Can't post? mdrun has been compiled with thread parallellization, so it runs in parallel on shared memory systems. I install Gromacs from fedora add-remove software package. configure:6274: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gromacs" | #define PACKAGE_TARNAME "gromacs" | #define PACKAGE_VERSION "4.5.4" | #define PACKAGE_STRING "gromacs 4.5.4" | #define have a peek at these guys

When I look in /usr/bin I can found all other command of gromacs but not g_mdrun_mpi... Thank you a lot for your patience to hear and a giving suggestion I have another query...Suppose now i install another new software and it also needed the LD_LIBRARY_PATH then in is I miss something,then please tell me.. Quote: Originally Posted by ramadavid Now when i am try to invoke openmpi with command mpirun ...Fedora respons with No such coomand ..

I > have had no trouble at all installing the sources on my linux box: The > configure and make scripts work perfectly. All binaries have names starting with g, for example mdrun has been renamed to gmdrun. x86_64-unknown-linux-gnu >>checking host system type... I also install open-mpi.

The response that you got on the mailing list is that the Fedora packages are not supported by the gromacs team, so they do not know capability of the Fedora versions. I installed >>>>fftw-2.1.5 >>>>then returned back to gromacs and gave the command: >>>>./configure --enable-mpi --with-fft=fftw2 >>>>the same result (pasted below). Privacy Policy | Term of Use | Posting Guidelines | Archive | Contact Us | Founding MembersPowered by vBulletin® Copyright ©2000 - 2012, vBulletin Solutions, Inc. Thank you a lot for help..

I install the openmpi1.6 and fftw3.3.2 to the /opt/openmpi-1.6 and /opt/fftw-3.3.2. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: 46 18 471 4205 fax: 46 18 511 755spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 Reply 3 Quote: It is working on single node, the add/remove software package of FEDORA- 17 is telling a different thing. yes >>>>checking for int...

If you are at an office or shared network, you can ask the network administrator to run a scan across the network looking for misconfigured or infected devices. The command Code: env will display them. With best wishes and regards Rama david ramadavid View Public Profile Find all posts by ramadavid #7 9th August 2012, 02:27 AM tashirosgt Offline Registered User Join Date: Now I understand that the packages have annotations which appear in a text window.

Groamac is working on threads... https://stat.ethz.ch/pipermail/r-help/2002-June/022710.html Any suggestions are > > appreciated! > > > > Yours > > Xin > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users Password Forgot Password? ramadavid View Public Profile Find all posts by ramadavid #2 6th August 2012, 05:35 PM tashirosgt Offline Registered User Join Date: Aug 2004 Posts: 4,016 Re: open-mpi gromacs

Next message: [gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)... More about the author CloudFlare Ray ID: 2fd8733cf6c322e8 • Your IP: • Performance & security by CloudFlare Configure: error: cannot compute sizeof (int) From The Open Source Backup Wiki (Amanda, MySQL Backup, BackupPC) Jump It certainly "saved my bacon" during this past academic quarter. See if Code: man pdb2gmx_mpi explains anything.

Thank you in advane.. The function of the two files is explained on the page: http://www.joshstaiger.org/archives/...rofile_vs.html __________________ "Never let the task you are trying to accomplish distract you from the study of computers." tashirosgt View This page has been accessed 10,500 times. check my blog So I am wonder what is the problem..????

What is next step... but i don't have this problem in windows majidraf Servers & Networking 11 23rd December 2010 08:24 PM OPEN VPN Problem efycaci Servers & Networking 22 27th January 2010 04:06 AM The man page for pdb2gmx_mpi may tell you this and it may explain how to include the path to the library files by using options with the command pdb2gmx_mpi.

yes >>>>checking whether mpicc accepts -O3 -fomit-frame-pointer - finline- >>>>functions -Wall -Wno-unused -funroll-all-loops...

If you're using a different compiler than was used to build glib, however, this will not work and will often cause this problem. configure: error: cannot compute sizeof (int) Explanation This is a follow-on error to problems with glib. Please don't post (un)subscribe requests to the list. mdrun has been compiled with thread parallellization (for running on a single node) and with Open MPI (for running on multiple nodes).

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Search Forums Show Threads Show Posts Tag Search Advanced Search Go to Page... N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" After configuring and making openmpi i started to configure gromacs. news Rama david ---------- Post added at 11:36 AM ---------- Previous post was at 08:14 AM ---------- Hi Fedora Friends...

Contents 1 Problem 2 Explanation 3 Solution 3.1 Different Compilers 3.2 Dependencies Problem [[email protected]]# ./configure --with-user=amandabackup --with-group=disk [...] checking size of int... o >>>>checking whether we are using the GNU C compiler... mpicc >>>>checking whether the MPI cc command works... configure:5529: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gromacs" | #define PACKAGE_TARNAME "gromacs" | #define PACKAGE_VERSION "4.5.4" | #define PACKAGE_STRING "gromacs 4.5.4" | #define

yes >>>>checking for unistd.h... Christian Burisch > Protein Mechanics and Evolution Group > CAS-MPG Partner Institute for Computational Biology > Shanghai Institutes for Biological Sciences > 320 Yue Yang Road > CN-200031 Shanghai > Tel: It doesn't have to be merely a single directory. After giving the command updatedb locate libmpi.so.1 [email protected] opt]# locate libmpi.so.1 /home/prashant/Desktop/software/openmpi/openmpi-1.6/ompi/.libs/libmpi.so.1 /home/prashant/Desktop/software/openmpi/openmpi-1.6/ompi/.libs/libmpi.so.1.0.3 /opt/openmpi-1.6/lib/libmpi.so.1 /opt/openmpi-1.6/lib/libmpi.so.1.0.3 /opt/openmpi-1.6/ompi/.libs/libmpi.so.1 /opt/openmpi-1.6/ompi/.libs/libmpi.so.1.0.3 /usr/local/lib/libmpi.so.1 /usr/local/lib/libmpi.so.1.0.3 But after giving the command pdb2gmx_mpi ..I stuck with the same problem

It is working on single node, the add/remove software package of FEDORA- 17 is telling a different thing. Thank you for reply andyour pations to listen me.. For growmacs, we find the followng annotation: Code: GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. mpicc -E >>>>checking whether mpicc accepts -O3...

It solve all the problem... I do not think your MPI compiler is working correctly. no >>>>checking for sys/types.h...