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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Wed Sep 11 2013 - 07:00:03 PDT
