Hi,
So just an update. Everything went fine. However, while running the test
for cuda I get this error consistently:
../../../../../bin/pmemd.cuda_SPFP: error while loading shared libraries:
libcurand.so.5.5: cannot open shared object file: No such file or directory
I think this is to do with the library and it might be solved by link
method and I have also included the path for libraries in my .bashrc file
export LD_LIBRARY_PATH=/usr/local/cuda-5.5/lib64:$LD_LIBRARY_PATH
Any suggestions where I am wrong?
Cheers,
Raman
On 11 November 2013 18:42, Raman Parkesh <rparkesh.gmail.com> wrote:
> Jason,
> Thanks for this. As you said I realized the possibility of broken amber
> tree so deleted the old amber12 directory and started a fresh copy of
> amber12 and was able to update with the command
> ./update_amber --update
>
> Configuration with gnu and make install went fine. Make test is going on
> and seems fine.
>
> I hope cuda compilation will go smoothly this time. Will keep udated about
> the progress.
>
> Cheers,
> Raman
>
>
> On 11 November 2013 17:42, Jason Swails <jason.swails.gmail.com> wrote:
>
>> On Mon, 2013-11-11 at 15:14 +0530, Raman Parkesh wrote:
>> > Hi,
>> > Further to the update error, I manually downloaded the bugfixes and
>> place
>> > them in the folder /home/samvit/bugfixes/12.0 and then manually updated
>> > them with the command
>> > ./update_amber --apply /home/samvit/bugfixes/12.0/bugfix xx
>> >
>> > It fixed upto bugfix 17 but I am not able to fix the bugfix 18.
>> >
>> > Preparing to apply a third-party update/patch... please wait.
>> > Applying bugfix.18.bz2
>> > PatchingError: .patches/ThirdParty12_Unapplied_Patches/bugfix.18 failed
>> to
>> > apply. No changes made from this patch
>>
>> Do not do this. The "--apply" flag is intended for third-party (and
>> other) extraneous patches, not for official updates. It is possible
>> that you have broken your tree and starting over from a fresh copy of
>> Amber 12 and AmberTools 13 is your best bet here.
>>
>> If the [[--update]] flag does not work, either your code has been
>> changed in a way that is incompatible with the updates, there is a
>> missing program (like `patch', `bunzip2', or `gunzip') that update_amber
>> needs to apply various updates. These should be fixed.
>>
>> 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 Mon Nov 11 2013 - 06:30:03 PST
