That's weird... that's arising because the PREC_MODEL variable is the null
string, or it's some kind of whitespace. Try this:
./test_amber_cuda.sh -1 SPDP
and see if that works...
On Tue, Apr 12, 2011 at 4:45 PM, Robert Wohlhueter <
bobwohlhueter.earthlink.net> wrote:
> Ross,
>
> Bravo! -- mostly. Your diagnosis was right on. I had patched amber11
> itself, but not the AmberTools1.4. Patching both as per you
> specification did the trick, and I got a completely successful compilation.
>
> But there remains a glitch in the `make test.cuda` part. The first time
> I ran it (see output copied below), it complained that
> "../../../bin/pmemd.cuda_: Command not found." Indeed, in
> $AMBERHOME/bin there is pmemd.cuda_SPDP executable to which pmemd.cuda
> is linked, but no pmemd.cuda_. I thought I could out-fox that by
> putting another link in that directory, namely of pmemd.cuda_SPDP to
> pmemd.cuda_. But simply running make test.cuda again gives the same
> error. I don't follow the intricacies of the 'test.cuda' makefile. Do
> I need to do some sort of a "make clean" before I can run the 'make
> test.cuda' a second time?
>
> Bob W.
>
>
> ******************************************************************************************************************************8
>
> root.winter-linux: ...amber11/src (45%)# cd ../test
> cd ../test
> root.winter-linux: ...amber11/test (46%)# make test.cuda
> make test.cuda
> (find . -name '*.dif' -o -name 'profile_mpi' | \
> while read dif ;\
> do \
> rm -f $dif ;\
> done ;\
> )
> rm -f TEST_FAILURES.diff
> ./test_amber_cuda.sh
> [: 35: unexpected operator
> [: 42: unexpected operator
> make[1]: Entering directory `/usr/local/lib/amber11/test'
> cd cuda && make -k test.pmemd.cuda GPU_ID= PREC_MODEL=
> make[2]: Entering directory `/usr/local/lib/amber11/test/cuda'
> ------------------------------------
> Running CUDA Implicit solvent tests.
> Precision Model =
> GPU_ID =
> ------------------------------------
> cd trpcage/ && ./Run_md_trpcage netcdf.mod
> ../../../bin/pmemd.cuda_: Command not found.0 file comparisons failed
>
> ./Run_md_trpcage: Program error
> make[2]: *** [test.pmemd.cuda.gb] Error 1
> cd gb_ala3/ && ./Run.igb1_ntc1_min netcdf.mod
> ../../../bin/pmemd.cuda_: Command not found.
> ./Run.igb1_ntc1_min: Program error
> make[2]: *** [test.pmemd.cuda.gb.serial] Error 1
> ------------------------------------
> Running CUDA Explicit solvent tests.
> Precision Model =
> GPU_ID =
> ------------------------------------
> cd 4096wat/ && ./Run.pure_wat netcdf.mod
> ../../../bin/pmemd.cuda_: Command not found.
> ./Run.pure_wat: Program error
> make[2]: *** [test.pmemd.cuda.pme] Error 1
> make[2]: Target `test.pmemd.cuda' not remade because of errors.
> make[2]: Leaving directory `/usr/local/lib/amber11/test/cuda'
> make[1]: *** [test.pmemd.cuda] Error 2
> make[1]: Target `test.serial.cuda' not remade because of errors.
> make[1]: Leaving directory `/usr/local/lib/amber11/test'
> 0 file comparisons passed
> 0 file comparisons failed
> 9 tests experienced errors
> Test log file saved as logs/test_amber_cuda/2011-04-12_19-02-35.log
> No test diffs to save!
> root.winter-linux: ...amber11/test (47%)# pwd
> pwd
> /usr/local/lib/amber11/test
> root.winter-linux: ...amber11/test (48%)#
>
>
>
> ***************************************************************************************
> On 4/12/11 6:27 PM, Ross Walker wrote:
> > Hi Robert,
> >
> > The Radix sort header file was removed by the latest patch however the
> problem you are seeing look suspiciously to me like the bugfixes were only
> partially applied. One possibility is that the patching was run with an
> AMBERHOME environment variable pointing to the wrong place.
> >
> > I suggest (for sanity) going back to the original tar files for Amber 11
> and AmberTools 1.4 and then patching and building cleanly from there. An
> example would be:
> >
> > ------------------------------------------
> >
> > cd $AMBERHOME
> > cd ..
> > rm -rf $AMBERHOME
> >
> > (Copy the original tar files here)
> >
> > tar xvjf AmberTools-1.4.tar.bz2
> > tar xvjf Amber11.tar.bz2
> >
> > cd $AMBERHOME
> >
> > wget http://ambermd.org/bugfixes/AmberTools/1.4/bugfix.all
> > patch -p0<bugfix.all
> > rm -f bugfix.all
> >
> > wget http://ambermd.org/bugfixes/11.0/bugfix.all
> > wget http://ambermd.org/bugfixes/11.0/apply_bugfix.x
> >
> > ./apply_bugfix.x bugfix.all
> >
> > cd $AMBERHOME/AmberTools/src
> >
> > ./configure -cuda gnu
> >
> > cd ../../src
> > make cuda
> >
> > cd ../test
> > make test.cuda
> >
> > ------------------------------------------
> >
> > Good luck,
> >
> > Ross
> >
> >> -----Original Message-----
> >> From: Robert Wohlhueter [mailto:bobwohlhueter.earthlink.net]
> >> Sent: Tuesday, April 12, 2011 9:19 AM
> >> To: amber.ambermd.org
> >> Subject: [AMBER] errors compiling amber11 for cuda
> >>
> >> Compiling AmberTools1.4 and amber11 on an AMD-64 4-core cpu under
> >> Ubuntu
> >> Linux 10.04 (after running bugfix.all, Apr. 12, 2011), with a GeForce
> >> GTX 275 card and with the latest cuda toolkit installed
> >> (cudatoolkit_3.2.16_linux_64_ubuntu10.04.run):
> >>
> >> The output from `configure` and `make` (copied below) seem to document
> >> the following successes and failures:
> >>
> >> 1) configuring for -cuda and gnu successfully generate a config.h file
> >> 2) cd'ing to the .../amber11/src dir and typing 'make cuda' initiates a
> >> lot of compilation work, apparently successful.
> >> 3) Until it get to make in dir
> >> /usr/local/lib/amber11/src/pmemd/src/cuda, where fatal erros are
> >> reported.
> >> 4) The errors seem to stem from the absence of radixsort.h, which is
> >> indeed not to be found in my $CUDA_HOME directory tree.
> >>
> >> Can anyone bail me out of the problem?
> >>
> >> Thanks, Bob Wohlhueter
> >>
> >> ***********************************************************************
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 12 2011 - 18:00:03 PDT
