Hello Murali, The chemistry programs Im using are
(1) NWChem (http://www.emsl.pnl.gov/docs/nwchem/nwchem.html) which is a free program. (2) GAMESS-UK (http://www.cfs.dl.ac.uk/) which is free for academics in the UK but the source code can be obtained freely under "Joint Software Development Licence". (3) Gaussian (http://www.gaussian.com/), commercial, I just use the serial version. Basicly, programs 1 and 2 are using the same tools for parallelization. For IO part, both use chemio. Im not really an expert on this but I can refer you to the following website: http://www-fp.mcs.anl.gov/chemio/ I can see now that chemio is originated from the same place where mpich, romio and pvfs2 are created :-). Thanks a lot, nasr On 9/20/06, Murali Vilayannur <[EMAIL PROTECTED]> wrote:
Hi Nasr, > Well, for the previous trials, the configuration step goes to > completion with no errors but the log file contains the errors you > saw. So I decided to proceed with the build and I could build mpich > 1.2.7p1 with intel compilers even though there are many warnings and I > hope ignoring them is safe. Oh I think it should be safe to ignore them if the build proceeds without any errors. Configure does a lot of checks and some of them are bound to fail. So unless we have reason to believe that they don't work, lets leave them alone. > To do a simple test, I compiled the benchmark "netpipe" using mpicc > and I could run it without any errors in a pvfs2 mount directory so > for now it looks fine. Hmm.. I suspect netpipe does not do any actual I/O to the pvfs2 file system. I think it would be good to run something like the attached program % mpicc io.c -g -Wall -o io % mpiexec -machinefile </path/to/machines/file> -n <number of processors> ./io -f </path/to/PVFS2/mount/point/file> -u -c -i 10 and hopefully you should be able to see that the program finishes and prints out results on how fast the operation went. > I have some questions about pvfs2. > > 1- After running the netpipe benchmark (as a user, not a root), when I > tried umount pvfs2 (as a root) I get "umount ..pvfs2 device is busy". > I waited for sometime and retried but the error still showing. If you cd'ed into the pvfs2 directory before running the netpipe benchmark, it is not possible to umount the directory without changing to a non-pvfs2 mounted directory. Basically, you cannot unmount if any process has a reference to any file on the pvfs2 volume. You could do % /usr/sbin/lsof /pvfs2/mount/point to get the names of all processes that have a reference to the mounted pvfs2 volume. After killing all those processes, you should be able to umount the volume. If you cannot unmount the volume still, then it is a bug and we will investigate that and fix it. > 2- Can I run executables from pvfs2 mount directory? My applications > are chemistry packages. I used to do the compiling in an NFS exported > directory, and I used my home directory as the working and scratch > directory but the executables remain in the /export directory. What is > the best approach under PVFS2? Yes, you can run executables off a pvfs2 mounted volume! You could keep both your executables and scratch data files on PVFS2, although I suspect it might be better (from a performance viewpoint) if you choose to keep executables on your home directory. Since we do not do any client-side caching (yet!), performance of small I/O's is not very good and hence running executables may not perform well with pvfs2. If you decide to use pvfs2 for executables, you could enable a client-side optimization by rerunning configure ./configure --enable-mmap-racache ..<usual arguments> This should improve performance quite a bit (i.e. running executables will benefit from this optimization) Hopefully, before the next release we should have a few more optimizations that will help workloads such as these. > Many thanks for your patience for a non-conputer-scientist like me > :-). I appreciate your help. No problem! Thanks for all the detailed reports! Please feel free to let us know if you hit any issues (performance, stability etc). Also, is it possible for you to describe what kind of access patterns we can expect from your chemistry applications? A rough overview is sufficient. Alternatively, are these apps available someplace? thanks, Murali > > nasr > > > > On 9/19/06, Murali Vilayannur <[EMAIL PROTECTED]> wrote: > > Hi Nasr, > > Something with your compiler/build environment must be broken..:( > > Does configure itself choke or does the subsequent make choke for you? > > If so, what was the exact error that you saw..? > > It increasingly looks like this may be an MPICH build problem or a build > > problem on your platform due to a buggy compiler etc.. > > thanks, > > Murali > > > > On Tue, 19 Sep 2006, Nasr Omar wrote: > > > > > Hello Murali, > > > > > > Attached is the configuration file for mpich2 1.0.4p1. The errors are > > > there just like in the case of mpich 1.2.7p1 I was trying to compile > > > earlier. > > > > > > Thanks in advance, > > > nasr > > > > > > > > > # cp /root/Desktop/cluster/mpich2-1.04p1/mpich2-1.0.4p1.tar.gz /usr/local/src > > > # cd /usr/local/src > > > # tar -xzf mpich2-1.0.4p1.tar.gz > > > # mkdir -p /opt/mpich2/gnu > > > # mkdir -p /tmp/mpich2/gnu > > > # export RSHCOMMAND=ssh > > > # export CFLAGS="-I/opt/pvfs2/include" > > > # export LDFLAGS="-L/opt/pvfs2/lib" > > > # export LIBS="-L/opt/pvfs2/lib -lpvfs2" > > > # cd /tmp/mpich2/gnu > > > # /usr/local/src/mpich2-1.0.4p1/configure --prefix=/opt/mpich2/gnu > > > --with-device=ch3:sock --enable-sharedlibs=gcc --enable-romio > > > --with-file-system=pvfs2+nfs+ufs --enable-f77 --enable-cxx > > > > > > > > > >
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