[gmx-users] Error while installing GROMACS-2018-rc1
Yongchul Chung
chung at northwestern.edu
Wed Jan 3 11:50:45 CET 2018
Well, celebrated too soon. I received the following error message during
"make check" step.
NOTE: The GPU has >25% less load than the CPU. This imbalance causes
performance loss.
Core t (s) Wall t (s) (%)
Time: 0.034 0.034 100.0
(ns/day) (hour/ns)
Performance: 53.584 0.448
Opened
/Users/ygchung/Desktop/codes/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr
as single precision energy file
Reading energy frame 20 time 0.020 Reading file
/Users/ygchung/Desktop/codes/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr,
VERSION 2018-rc1-dev-20180103-871f2f460-unknown (single precision)
Can not increase nstlist because an NVE ensemble is used
Using 1 MPI thread
1 GPU auto-selected for this run.
Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
PP:0
Compilation of source file
/Users/ygchung/Desktop/codes/gromacs/src/gromacs/mdlib/nbnxn_ocl/
nbnxn_ocl_kernels.cl failed!
-- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
-DGMX_OCL_FASTGEN_ADD_TWINCUT -DEL_EWALD_ANA -DEELNAME=_ElecEw
-DVDWNAME=_VdwLJ -DCENTRAL=22 -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8
-DNBNXN_GPU_CLUSTER_SIZE=8 -DNBNXN_GPU_JGROUP_SIZE=4
-DGMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY=4 -DNBNXN_MIN_RSQ=3.82e-07f
-DIATYPE_SHMEM -cl-fast-relaxed-math
-I/Users/ygchung/Desktop/codes/gromacs/src/gromacs/mdlib/nbnxn_ocl
--------------LOG START---------------
<program source>:80:10: fatal error: 'nbnxn_ocl_kernel_pruneonly.clh' file
not found
#include "nbnxn_ocl_kernel_pruneonly.clh"
^
---------------LOG END----------------
-------------------------------------------------------
Program: mdrun-test, version 2018-rc1-dev-20180103-871f2f460-unknown
Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 502)
Function: cl_program gmx::ocl::compileProgram(FILE *, const std::string
&, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)
Internal error (bug):
Failed to compile NBNXN kernels for GPU #AMD Radeon Pro 560 Compute Engine
Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Start 33: MdrunMpiTests
33/39 Test #33: MdrunMpiTests .................... Passed 2.69 sec
Start 34: regressiontests/simple
34/39 Test #34: regressiontests/simple ........... Passed 2.33 sec
Start 35: regressiontests/complex
35/39 Test #35: regressiontests/complex .......... Passed 53.42 sec
Start 36: regressiontests/kernel
36/39 Test #36: regressiontests/kernel ........... Passed 32.33 sec
Start 37: regressiontests/freeenergy
37/39 Test #37: regressiontests/freeenergy ....... Passed 5.70 sec
Start 38: regressiontests/pdb2gmx
38/39 Test #38: regressiontests/pdb2gmx .......... Passed 15.66 sec
Start 39: regressiontests/rotation
39/39 Test #39: regressiontests/rotation ......... Passed 3.10 sec
97% tests passed, 1 tests failed out of 39
Label Time Summary:
GTest = 19.86 sec*proc (33 tests)
IntegrationTest = 18.38 sec*proc (3 tests)
MpiTest = 2.73 sec*proc (3 tests)
UnitTest = 1.48 sec*proc (30 tests)
Total Test time (real) = 132.48 sec
The following tests FAILED:
32 - MdrunTests (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
make: *** [check] Error 2
On Wed, Jan 3, 2018 at 7:42 PM, Yongchul Chung <chung at northwestern.edu>
wrote:
> Thanks, I have successfully installed the release-2018 version of GROMACS
> on Macbook Pro 2017 HighSierra.
>
>
> On Tue, Jan 2, 2018 at 1:43 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> Thanks, we have found and prepared a fix for an issue that looks very
>> similar (https://gerrit.gromacs.org/#/c/7400). Apparently the Mac OpenCL
>> compilation cannot tolerate any extra spaces in the command used to
>> compile
>> the kernels used on the device.
>>
>> You could either compile GROMACS without OpenCL support for now, or if you
>> would like to see if we have fixed the issue for you, that link enables
>> you
>> to download a tarball that contains the fix! We'd love to hear that it
>> works.
>>
>> Mark
>>
>> On Mon, Jan 1, 2018, 20:05 Yongchul Chung <chung at northwestern.edu> wrote:
>>
>> > I am trying to install the latest GROMACS on Macbook Pro 2017 15-inch
>> (High
>> > Sierra) and got the following error message when issuing "make" command
>> > during the installation steps.
>> >
>> > My command for cmake was: cmake .. -DGMX_BUILD_OWN_FFTW=ON
>> > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DGMX_USE_OPENCL=ON
>> >
>> > Thanks in advance for the help.
>> >
>> > [ 91%] Building CXX object
>> >
>> > src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_ocl/nbnxn_
>> ocl_data_mgmt.cpp.o
>> >
>> > In file included from
>> >
>> > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/md
>> lib/nbnxn_ocl/nbnxn_ocl_data_mgmt.cpp:54:
>> >
>> > In file included from
>> >
>> > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/gp
>> u_utils/oclutils.h:46:
>> >
>> > In file included from
>> >
>> > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/gp
>> u_utils/gmxopencl.h:61:
>> >
>> > In file included from
>> > /System/Library/Frameworks/OpenCL.framework/Headers/opencl.h:16:
>> >
>> > In file included from
>> > /System/Library/Frameworks/OpenCL.framework/Headers/gcl.h:23:
>> >
>> > */usr/include/dispatch/dispatch.h:38:45: **error: **expected value in
>> > expression*
>> >
>> > #if !defined(HAVE_UNISTD_H) || HAVE_UNISTD_H
>> >
>> > * ^*
>> >
>> > 1 error generated.
>> >
>> > make[2]: ***
>> >
>> > [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_ocl/
>> nbnxn_ocl_data_mgmt.cpp.o]
>> > Error 1
>> >
>> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
>> >
>> > make: *** [all] Error 2
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-request at gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
More information about the gromacs.org_gmx-users
mailing list