simtk.org

I got the following failures when I did make test.

The following tests FAILED:
25 - TestCudaEwald (Failed)
26 - TestCudaCustomTorsionForce (Failed)
27 - TestCudaGBSAOBCForce (Failed)
28 - TestCudaGBVIForce (Failed)
29 - TestCudaHarmonicAngleForce (Failed)
30 - TestCudaCMMotionRemover (Failed)
31 - TestCudaLangevinIntegrator (Failed)
32 - TestCudaRBTorsionForce (Failed)
33 - TestCudaVariableVerletIntegrator (Failed)
34 - TestCudaVariableLangevinIntegrator (Failed)
35 - TestCudaCustomAngleForce (Failed)
36 - TestCudaNonbondedForce (Failed)
37 - TestCudaRandom (Failed)
38 - TestCudaPeriodicTorsionForce (Failed)
39 - TestCudaBrownianIntegrator (Failed)
40 - TestCudaCustomExternalForce (Failed)
41 - TestCudaHarmonicBondForce (Failed)
42 - TestCudaCustomNonbondedForce (Failed)
43 - TestCudaSettle (Failed)
44 - TestCudaAndersenThermostat (Failed)
45 - TestCudaVerletIntegrator (Failed)
46 - TestCudaCustomBondForce (Failed)
47 - TestCudaUsingParameterFile (Failed)
49 - TestCudaGBVISoftcoreForce (Failed)
50 - TestCudaUsingParameterFile (Failed)
Errors while running CTest
make: *** [test] Error 8
[root@localhost build_openmm]#

Hmm. It looks like all of the Cuda tests are failing. Do the cuda test programs such as deviceQuery, which should be in the cuda sdk, work correctly?

I am having trouble compiling the sdk

[root@localhost C]# make
make[1]: Entering directory `/root/NVIDIA_GPU_Computing_SDK/C/common'
make[1]: Leaving directory `/root/NVIDIA_GPU_Computing_SDK/C/common'
make[1]: Entering directory `/root/NVIDIA_GPU_Computing_SDK/C/common'
make[1]: Leaving directory `/root/NVIDIA_GPU_Computing_SDK/C/common'
make[1]: Entering directory `/root/NVIDIA_GPU_Computing_SDK/C/common'
make[1]: Leaving directory `/root/NVIDIA_GPU_Computing_SDK/C/common'
make[1]: Entering directory `/root/NVIDIA_GPU_Computing_SDK/shared'
make[1]: Leaving directory `/root/NVIDIA_GPU_Computing_SDK/shared'
make -C src/asyncAPI/
make[1]: Entering directory `/root/NVIDIA_GPU_Computing_SDK/C/src/asyncAPI'
nvcc fatal : Unsupported gpu architecture 'compute_20'
make[1]: *** [obj/i386/release/asyncAPI.cu.o] Error 255
make[1]: Leaving directory `/root/NVIDIA_GPU_Computing_SDK/C/src/asyncAPI'
make: *** [src/asyncAPI/Makefile.ph_build] Error 2
[root@localhost C]#

It was missing the library path.

I am trying to compile gromacs openmm now and it does not seem to compile md_openmm. I set the library path

$LD_LIBRARY_PATH
/usr/local/openmm/lib/:/usr/local/cuda/lib:
[root@localhost gromacs-4.0.7]#

Making all in kernel
make[3]: Entering directory `/root/Download/gromacs-4.0.7/src/kernel'
/bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o mdrun glaasje.o gctio.o ionize.o do_gct.o repl_ex.o xutils.o md.o mdrun.o genalg.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la -lxml2 -lnsl -lfftw3f -lm -lSM -lICE -lX11
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o mdrun glaasje.o gctio.o ionize.o do_gct.o repl_ex.o xutils.o md.o mdrun.o genalg.o ./.libs/libgmxpreprocess.a ../mdlib/.libs/libmd.a /root/Download/gromacs-4.0.7/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a -lxml2 -lnsl -lfftw3f -lm -lSM -lICE -lX11
md.o: In function `do_md':
md.c:(.text+0x64c): undefined reference to `openmm_init'
md.c:(.text+0xd7f): undefined reference to `openmm_take_one_step'
md.c:(.text+0xf05): undefined reference to `openmm_copy_state'
md.c:(.text+0x1423): undefined reference to `openmm_cleanup'
collect2: ld returned 1 exit status
make[3]: *** [mdrun] Error 1
make[3]: Leaving directory `/root/Download/gromacs-4.0.7/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/root/Download/gromacs-4.0.7/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/root/Download/gromacs-4.0.7/src'
make: *** [all-recursive] Error 1
[root@localhost gromacs-4.0.7]# echo

I think the problem is I only have double precision libraries

[root@localhost build_openmm]# ls /usr/local/openmm/lib/
libOpenMM_d.so libOpenMMFreeEnergy_d.so libOpenMMFreeEnergy_static_d.a libOpenMM_static_d.a plugins

Is there a way to build single precision?

Jack, the "_d" stands for "Debug" - those are debug libraries, not double precision. You need to change the "Debug" to "Release" in the CMake file to build the release libraries. Regards, Sherm

You are right. I switched from Debug to Release in cmake advance options.

[root@localhost build_openmm]# ls /usr/local/openmm/lib/
libOpenMM_d.so libOpenMMFreeEnergy_d.so libOpenMMFreeEnergy.so libOpenMMFreeEnergy_static.a libOpenMMFreeEnergy_static_d.a libOpenMM.so libOpenMM_static.a libOpenMM_static_d.a plugins

Still having trouble compiling gromacs. I copied these source files, md_openmm.h, md_openmm.cpp md.c over to the src/kernel on my gromacs distribution. If does not compile unless i comment out the preprocessor condition

/*
#define USE_OPENMM
#ifdef USE_OPENMM
*/

#include "md_openmm.h"

/*
#endif
*/

but then i dont see md_openmm among the binaries. Does it just build as mdrun?

I tried compiling it with this flag hoping it would see this header
./configure CPPFLAGS="-DUSE_OPENMM"

But it did not compile

make[3]: Entering directory `/root/Download/gromacs-4.0.7/src/kernel'
/bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o mdrun glaasje.o gctio.o ionize.o do_gct.o repl_ex.o xutils.o md.o mdrun.o genalg.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la -lxml2 -lnsl -lfftw3f -lm -lSM -lICE -lX11
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o mdrun glaasje.o gctio.o ionize.o do_gct.o repl_ex.o xutils.o md.o mdrun.o genalg.o ./.libs/libgmxpreprocess.a ../mdlib/.libs/libmd.a /root/Download/gromacs-4.0.7/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a -lxml2 -lnsl -lfftw3f -lm -lSM -lICE -lX11
md.o: In function `do_md':
md.c:(.text+0x64c): undefined reference to `openmm_init'
md.c:(.text+0xd7f): undefined reference to `openmm_take_one_step'
md.c:(.text+0xf05): undefined reference to `openmm_copy_state'
md.c:(.text+0x1423): undefined reference to `openmm_cleanup'
collect2: ld returned 1 exit status
make[3]: *** [mdrun] Error 1
make[3]: Leaving directory `/root/Download/gromacs-4.0.7/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/root/Download/gromacs-4.0.7/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/root/Download/gromacs-4.0.7/src'
make: *** [all-recursive] Error 1

> Does it just build as mdrun?

Correct. We manually rename it to mdrun-openmm.

After copying the modified files for OpenMM into your Gromacs source directory, did you remember to rerun automake and autoconf? That's necessary, since one of the modified files is a Makefile.am.

Peter

I'm not sure how to regenerate the build system

[root@localhost gromacs-4.0.7]# automake
aclocal.m4:14: error: this file was generated for autoconf 2.61.
You have another version of autoconf. If you want to use that,
you should regenerate the build system entirely.
aclocal.m4:14: the top level
autom4te: /usr/bin/m4 failed with exit status: 63
automake: autoconf failed with exit status: 63

[root@localhost gromacs-4.0.7]# autoconf
aclocal.m4:14: error: this file was generated for autoconf 2.61.
You have another version of autoconf. If you want to use that,
you should regenerate the build system entirely.
aclocal.m4:14: the top level
autom4te: /usr/bin/m4 failed with exit status: 63
[root@localhost gromacs-4.0.7]#