On 09/11/2013 04:14 PM, Sanjib Paul wrote:
> 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.
You are obviously using an old configure_mpich2 script (in my
installation, this script searches for a mpich* directory, in your
installation it probably looks for mpich2*).
You might just want to rename your mpich-3.0.4 directory to
mpich2-3.0.4. Alternatively, modify the corresponding part of the
configure 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
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
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>>>
>>>
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>>
>>
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Received on Wed Sep 11 2013 - 08:00:03 PDT
