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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.
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: 18.104.22.168 • 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).
Google™ Search FedoraForum Search Red Hat Bugzilla Search 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...