On 09/11/2013 04:04 PM, Sanjib Paul 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.
Then you should probably delete all mpich2-1.5-3.* artifacts. Or, if you
are not sure anymore what you are doing, better delete the entire Amber
tree an restart from scratch.
>
> 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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Received on Wed Sep 11 2013 - 07:30:04 PDT
