Thank you Ross. Patching the AmberTools as well did the trick.
Just to be sure, I didn't recompile everything, just the cuda part. That means I didn't do the first two lines below (tar xzvj Amber11.tar.bz2; tar xzvj AmberTools-1.5.tar.bz2). This should be alright?
--Farid
________________________________________
From: Ross Walker [ross.rosswalker.co.uk]
Sent: Friday, August 19, 2011 12:20 PM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] Major GPU Update Released
Did you patch AMBERTools as well? - You need AMBER Tools 1.5 and you must
have applied ALL the latest bugfixes for that, up to and including
bugfix.13.
The exact patching procedure is:
tar xvjf Amber11.tar.bz2
tar xvjf AmberTools-1.5.tar.bz2
export AMBERHOME=~/amber11
wget
http://ambermd.org/bugfixes/11.0/bugfix.1to17.tar.bz2
wget
http://ambermd.org/bugfixes/11.0/apply_bugfix.x
chmod 700 apply_bugfix.x
./apply_bugfix.x bugfix.1to17.tar.bz2
wget
http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all
cd $AMBERHOME
patch -p0 < ../bugfix.all
All the best
Ross
> -----Original Message-----
> From: Ismail, Mohd F. [mailto:farid.ou.edu]
> Sent: Friday, August 19, 2011 10:15 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Major GPU Update Released
>
> I'm getting the error undefined reference to `curandCreateGenerator'
> error with the update when I try to recompile. The exact error
> message:
>
> ./cuda/cuda.a(gpu.o): In function `gpu_armset_':
> gpu.cpp:(.text+0x2548): undefined reference to `curandCreateGenerator'
> gpu.cpp:(.text+0x255e): undefined reference to
> `curandSetPseudoRandomGeneratorSeed'
> ./cuda/cuda.a(kForcesUpdate.o): In function `kRandom':
> tmpxft_000007802_000000000000-
> 4_kForcesUpdate.compute_13.cudafe1.cpp:(.text+0x325d): undefined
> reference to `curandGenerateNormalDouble'
> collect2: ld returned 1 exit status
> make[2]: *** [pmemd.cuda] Error 1
> make[2]: Leaving directory `/usr/local/amber11/src/pmemd/src'
> make[1]: *** [cuda] Error 2
> make[1]: Leaving directory `/usr/local/amber11/src/pmemd'
> make: *** [cuda] Error 2
>
> My system is a dual opteron with GTX 590, cuda toolkit version 3.2 and
> 4.0 (switched to appropriately when needed), and gcc 4.5 and 4.3 (if I
> use toolkit 4.0 it will whine about gcc4.5).
>
> Help please.
>
>
> Farid Ismail
> ________________________________________
> From: Ross Walker [ross.rosswalker.co.uk]
> Sent: Friday, August 19, 2011 10:22 AM
> To: AMBER Mailing List
> Subject: [AMBER] Major GPU Update Released
>
> Dear Fellow Amberites,
>
> After several months of promising I am now pleased to announce that we
> have
> released a major update to the GPU accelerated PMEMD code in AMBER and
> I
> would encourage you to update your code. This update, ostensibly
> labeled
> bugfix.17, almost doubles performance for PME calculations, without
> introducing any new approximations, while also adding support for extra
> points and fixing a number of outstanding bugs related to the use NPT
> with
> restraints and organic solvents. It also addresses the issues with runs
> locking up on GTX4XX and 5XX cards in a way that does not impact
> performance
> on other GPUs. Full details of the GPU implementation and updated
> benchmarks
> are available on http://ambermd.org/gpus/
>
> Some example performance improvements are () show old performance
> numbers:
>
> Performance in (ns/day)
> 1xC2070 2xC2070 4xC2070 8xC2070
> 1xGTX580
> 2xGTX580
> JAC prod NVE 35.7 (21.1) 49.2 (31.0) 69.7 (44.4) 85.2 (52.7) 50.8
> 67.6
> JAC prod NPT 30.0 (18.5) 40.7 (27.3) 55.5 (38.4) 67.8 (45.6) 40.7
> 55.2
> Factor IX NVE 11.1 (5.3) 14.8 (8.8) 21.2 (14.0) 29.3 (20.2) 14.3
> 18.5
> Factor IX NPT 9.0 (4.4) 12.2 (6.5) 17.8 (8.8) 20.5 (10.9) 11.8
> 16.0
> Cellulose NPT 2.0 (1.1) 2.9 (1.7) 4.2 (2.6) 5.9 (3.8)
> Insuf
> Mem
>
> I intend to post some example hardware configurations on the GPU
> section of
> the Amber website and, in collaboration with NVIDIA and certain
> hardware
> vendors, we will shortly have hardware configurations available, termed
> MD
> SimCluster(s), that can be purchased with AMBER preinstalled. I will
> post
> more details on this program once it is formally announced.
>
> The specifics of the update are as follows:
>
> -----------------------------------------------------------------------
> -----
> --
> ********>Bugfix 17:
> Author: Ross Walker & Scott Le Grand
> Date: 18 Aug 2011
>
> Programs: pmemd.cuda
>
> Description: Major update. Updates cuda implementation to v2.2. This
> patch
> provides
> a significant update to the GPU support. It more than
> doubles
> performance
> across the board, fixes numerous bugs, especially
> involving
> NPT.
>
> Performance notes:
>
> Full benchmarks are available on http://ambermd.org/gpus/
>
> Some brief examples of the performance improvements are:
>
> i) JAC Production NVE - 1xC2070 35.70ns/day (new
> code),
> 21.11ns/day (old code)
> 8xC2070 85.70nd/day (new
> code),
> 52.68ns/day (old code)
> ii) FactorIX Production NVE - 1xC2070 11.08ns/day (new
> code),
> 5.30ns/day (old code)
> 8xC2070 29.30nd/day (new
> code),
> 20.20ns/day (old code)
>
> Updates include:
>
> 1) Updated the setting for no_ntt3_sync when ig=-1 -
> remove
> ifdef NO_NTT3_SYNC
> This update applies to both CPU and GPU and will
> improve
> scaling considerably
> in both cases.
>
> 2) Support for extra points added to GPU code [serial
> only]
> (single extra point e.g. TIP4PEW)
>
> 3) Power of 2 limitation on GPU count is removed. Both GB
> and
> PME can now use
> 1,2,3,4,5 etc GPUs.
>
> 4) NTT=2 is now accelerated on GPU.
>
> 5) Check that ATOMS_PER_MOLECULE sums to NATOM for
> constant
> pressure to test
> for bogus prmtops. Applies to both CPU and GPU code.
>
> 6) Use CURAND from CUDA toolkit in place of built in
> random
> number generator.
>
> 7) Multiple bug fixes including:
> i) Fixes NPT restraint issues leading to kernel launch
> failures.
> ii) Fix MPI energy differences due to missing initial
> backwards half step.
> iii) Fix certain SM2.0 series crashes for PME runs with
> > 8A
> cutoff
> iv) Fixes 8 node NPT crash
> v) Multiple other minor bug fixes.
>
> 8) Performance for PME simulations is improved by between
> 1.8
> and 2.2x both in
> serial and parallel.
>
> 9) Support CUDA 4.0 compiler.
>
> 10) Fixes kReduceSoluteCOM error when running with large
> numbers of solute molecules
> or many solvent molecules with atom counts > 3. The
> previous limit of 460 on C1060
> and 1535 on C20xx has been removed although
> performance
> will be impacted if you have
> more molecules with >3 atoms in your system.
>
> 11) Introduces permanent lockup fix for GTX5XX and GTX4XX
> cards without impacting
> performance as the previous worksaround did.
>
> 12) Adds files necessary for Windows build of GPU
> accelerated
> code to be described
> on the AMBER Website shortly.
>
> -----------------------------------------------------------------------
> -----
> --
>
> You can obtain the update from http://ambermd.org/bugfixes11.html
>
> Comments are welcome.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may
> not
> be read every day, and should not be used for urgent or sensitive
> issues.
>
>
>
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Received on Fri Aug 19 2011 - 11:00:05 PDT
