Hello,
Sorry, I have written wrong. After extracting mpich-3.0.4.tar.gz
and running the script configure_mpich2, I am getting the following message.
$./configure_mpich2 gnu
Setting AMBERHOME to /home/software/AMBER12/amber12
You must download MPICH2 and extract it here
(for example, type 'tar xvfz mpich2-1.4.1p1.tar.gz')
See
http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloadsfor
more info;
Then, re-run this script.
But I am getting only mpich not mpich2. So, what should I do? Please help.
On Wed, Sep 11, 2013 at 7:34 PM, Sanjib Paul <sanjib88paul.gmail.com> wrote:
> Hello,
> This time I have downloaded mpich-3.0.4.tar.gz. And followed the
> same procedure. But I am getting the same error which I got last time.
>
> Sanjib
>
>
> On Wed, Sep 11, 2013 at 7:08 PM, Jan-Philip Gehrcke <
> jgehrcke.googlemail.com> wrote:
>
>> Hello!
>>
>> On 09/11/2013 03:28 PM, Sanjib Paul wrote:
>> > Hello,
>> > I have downloaded a file named 'mpich2-1.5-3.fc20.x86_64.rpm',
>> > extracted it.
>>
>> You have downloaded a binary package of that software. What you need is
>> the source distribution, which is usually offered as gzipped tarball
>> (these filenames usually end with .tar.gz). When you extract such an
>> archive, the top-level directory usually contains a `configure` file.
>>
>> This one is obviously missing in your case, see the error message below.
>>
>> Cheers!
>>
>>
>> > And then kept the extracted file 'mpich2-1.5-3.fc20.x86_64'
>> > in $AMBERHOME/AmberTools/src folder. Then run the script
>> configure_mpich2.
>> >
>> > ./configure_mpich2 gnu
>> >
>> > Setting AMBERHOME to /home/software/AMBER12/amber12
>> >
>> > ./configure_mpich2: line 141: ./configure: No such file or directory
>> > MPICH2 configure failed, returning 127
>> >
>> > I am getting the above error. I have searched google, but did not get
>> any
>> > problem or answer regarding this. So, please help.
>> >
>> > Sanjib
>> >
>> >
>> >
>> >
>> > On Wed, Sep 4, 2013 at 8:26 PM, Jason Swails <jason.swails.gmail.com>
>> wrote:
>> >
>> >> On Wed, Sep 4, 2013 at 10:21 AM, Sanjib Paul <sanjib88paul.gmail.com>
>> >> wrote:
>> >>
>> >>> Hello,
>> >>> Thanks for your valuable suggestion. After updating we are
>> able
>> >> to
>> >>> run AMBER12 (sander, pmemd, sander.MPI & pmemd.MPI, pmemd.cuda). But
>> >>> unfortunately when we are not able to install pmemd.cuda.MPI
>> >> successfully.
>> >>> Those are few following errors which we are getting at the end of
>> >>> installation process.
>> >>>
>> >>> ./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Clone()
>> const':
>> >>> gpu.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone()
>> >>> const]+0x27): undefined reference to `MPI::Comm::Comm()'
>> >>>
>> >>>
>> >>
>> ./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI9Intracomm5SplitEii[MPI::Intracomm::Split(int,
>> >>> int) const]+0x24): more undefined references to `MPI::Comm::Comm()'
>> >> follow
>> >>> ./cuda/cuda.a(gpu.o):(.rodata._ZTVN3MPI3WinE[vtable for
>> MPI::Win]+0x48):
>> >>> undefined reference to `MPI::Win::Free()'
>> >>> ./cuda/cuda.a(gpu.o):(.rodata._ZTVN3MPI8DatatypeE[vtable for
>> >>> MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>> >>> collect2: ld returned 1 exit status
>> >>> make[3]: *** [pmemd.cuda.MPI] Error 1
>> >>> make[3]: Leaving directory `/home/test/amber12/src/pmemd/src'
>> >>> make[2]: *** [cuda_parallel] Error 2
>> >>> make[2]: Leaving directory `/home/test/amber12/src/pmemd'
>> >>> make[1]: *** [cuda_parallel] Error 2
>> >>> make[1]: Leaving directory `/home/test/amber12/src'
>> >>> make: *** [install] Error 2
>> >>>
>> >>> We are using cuda version 5.5 with openmpi 1.7.2 built with installed
>> >> cuda.
>> >>> We did not understand what the problem is. Please give some
>> suggestion.
>> >>>
>> >>
>> >> It's likely that your MPI was not built with the appropriate support
>> that
>> >> pmemd.cuda.MPI needs (make sure the MPI is built with C++ support, I
>> >> think). I've been using mpich2 (now just 'mpich') for some time and
>> I've
>> >> never had a problem building pmemd.cuda.MPI before. Note, if you
>> google
>> >> the last little bit of your error message:
>> >>
>> >> ./cuda/cuda.a(gpu.o):(.rodata._ZTVN3MPI8DatatypeE[vtable for
>> >> MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>> >>
>> >> it brings you to this link:
>> http://archive.ambermd.org/201106/0678.html
>> >>
>> >> which provides useful things to try.
>> >>
>> >> Try adding -lmpi_cxx to the PMEMD_CU_LIBS line in config.h. If that
>> still
>> >> doesn't work, rebuild your MPI with C++ support. If you are unsure
>> what to
>> >> do, use the configure_mpich2 script in $AMBERHOME/AmberTools/src to
>> build
>> >> your own MPI (see the manual for instructions -- you need to download
>> >> mpich2 first to use it). You also need to set up PATH and
>> LD_LIBRARY_PATH
>> >> so that "which mpif90" returns the version in $AMBERHOME/bin.
>> >>
>> >> HTH,
>> >> Jason
>> >>
>> >> --
>> >> Jason M. Swails
>> >> BioMaPS,
>> >> Rutgers University
>> >> Postdoctoral Researcher
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>> >>
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>> >
>>
>>
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>
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Received on Wed Sep 11 2013 - 07:30:05 PDT
