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Date:
2013-05-07 14:02
Priority:
3
State:
Open
Submitted by:
Mark Williamson (mjw)
Assigned to:
Nobody (None)
Resolution:
None
Summary:
Various "make test" tests fail if environment variables pertaining to an existing install of OpenMM are present

Detailed description
OK, this is quite a subjective one (hence feel free to close), since this is a user error at the end of the day, but resolving this may reduce the number of false positives with respect to unit testing of OpenMM, particularly within a cluster environment that may have multiple versions of OpenMM installed.

So, if one compiles a build of OpenMM i.e.:

$ unzip OpenMM5.1-Source.zip
$ mkdir OpenMM5.1-Build
$ cd OpenMM5.1-Build
$ cmake -DCMAKE_INSTALL_PREFIX=/usr/local/OpenMM5.1 -DCUDA_BUILD_CUBIN="OFF" ../OpenMM5.1-Source

<time passes>

and then one runs a "make test", some of the tests will fail, because there are stray environment variables pertaining to an *older* version of OpenMM.

For instance, if the environment is set, pointing to an existing 5.0 install:

export OPENMM_HOME=/usr/local/OpenMM5.0
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$OPENMM_HOME/lib:$OPENMM_HOME/lib/plugins
export OPENMM_PLUGIN_DIR=$OPENMM_HOME/lib/plugins

and one repeats the above building of the the RC2 release:

$ md5sum OpenMM5.1RC2-Source.zip
a65a0dd94fdff12789261313ba7d5879 OpenMM5.1RC2-Source.zip

The following tests will fail:
196 - TestOpenCLVariableLangevinIntegratorMixed (Failed)
219 - TestOpenCLNonbondedForce2 (OTHER_FAULT)
220 - TestOpenCLGBSAOBCForce2Single (OTHER_FAULT)
221 - TestOpenCLGBSAOBCForce2Mixed (OTHER_FAULT)
222 - TestOpenCLGBSAOBCForce2Double (OTHER_FAULT)

Running some of the tests individually:

$ ./TestOpenCLNonbondedForce2
Nonbonded test: system size=2000 nonbonded method=CutoffNonPeriodic exception: clCreateKernel
Nonbonded test: system size=2000 nonbonded method=CutoffPeriodic exception: clCreateKernel
Nonbonded test: system size=2000 nonbonded method=Ewald exception: clCreateKernel
*** glibc detected *** ./TestOpenCLNonbondedForce2: double free or corruption (!prev): 0x000000000267d5d0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f12ad284b96]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZNSsD1Ev+0x23)[0x7f12adb75c13]
/lib/x86_64-linux-gnu/libc.so.6(+0x3b901)[0x7f12ad241901]
/lib/x86_64-linux-gnu/libc.so.6(+0x3b985)[0x7f12ad241985]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf4)[0x7f12ad227774]
./TestOpenCLNonbondedForce2[0x409c91]
======= Memory map: ========
00400000-00422000 r-xp 00000000 08:01 950710 /tmp/OpenMM5.1RC2-Build/TestOpenCLNonbondedForce2
00622000-00623000 r--p 00022000 08:01 950710 /tmp/OpenMM5.1RC2-Build/TestOpenCLNonbondedForce2
00623000-00624000 rw-p 00023000 08:01 950710 /tmp/OpenMM5.1RC2-Build/TestOpenCLNonbondedForce2
0251c000-035b0000 rw-p 00000000 00:00 0 [heap]
200000000-e00000000 ---p 00000000 00:00 0
7f1299bfb000-7f1299cfb000 rw-p 00000000 00:00 0
7f1299cfb000-7f1299cfc000 ---p 00000000 00:00 0
7f1299cfc000-7f129a4fc000 rwxp 00000000 00:00 0
7f129a4fc000-7f129a4fd000 ---p 00000000 00:00 0
7f129a4fd000-7f129acfd000 rwxp 00000000 00:00 0
7f129acfd000-7f129acfe000 ---p 00000000 00:00 0
7f129acfe000-7f129b4fe000 rwxp 00000000 00:00 0
7f129b4fe000-7f129b4ff000 ---p 00000000 00:00 0
7f129b4ff000-7f129bcff000 rwxp 00000000 00:00 0
7f129bcff000-7f129bd00000 ---p 00000000 00:00 0
7f129bd00000-7f129c500000 rwxp 00000000 00:00 0
7f129c500000-7f129c501000 ---p 00000000 00:00 0
7f129c501000-7f129cd01000 rwxp 00000000 00:00 0
7f129cd01000-7f129d103000 rw-s 6019a8000 00:05 14797 /dev/nvidia0
7f129d103000-7f129d505000 rw-s 3d5c11000 00:05 14797 /dev/nvidia0
7f129d505000-7f129d907000 rw-s 3b320c000 00:05 14797 /dev/nvidia0
7f129d907000-7f129d908000 ---p 00000000 00:00 0
7f129d908000-7f129e108000 rwxp 00000000 00:00 0
7f129e108000-7f129e208000 rw-p 00000000 00:00 0
7f129e208000-7f129e209000 ---p 00000000 00:00 0
7f129e209000-7f129ea09000 rwxp 00000000 00:00 0
7f129ea09000-7f129ea0a000 ---p 00000000 00:00 0
7f129ea0a000-7f129f20a000 rwxp 00000000 00:00 0
7f129f20a000-7f129f20b000 ---p 00000000 00:00 0
7f129f20b000-7f129fa0b000 rwxp 00000000 00:00 0
7f129fa0b000-7f129fa0c000 ---p 00000000 00:00 0
7f129fa0c000-7f12a020c000 rwxp 00000000 00:00 0
7f12a020c000-7f12a020d000 ---p 00000000 00:00 0
7f12a020d000-7f12a0a0d000 rwxp 00000000 00:00 0
7f12a0a0d000-7f12a0a0e000 ---p 00000000 00:00 0
7f12a0a0e000-7f12a120e000 rwxp 00000000 00:00 0
7f12a120e000-7f12a130e000 rw-p 00000000 00:00 0
7f12a130e000-7f12a140e000 rw-s 5fd770000 00:05 14797 /dev/nvidia0
7f12a140e000-7f12a150e000 rw-p 00000000 00:00 0
7f12a150e000-7f12a160e000 rw-s 482f76000 00:05 14797 /dev/nvidia0
7f12a160e000-7f12a170e000 rw-p 00000000 00:00 0
7f12a170e000-7f12a170f000 rw-s dfee6000 00:05 14797 /dev/nvidia0
7f12a170f000-7f12a1710000 rw-s 482f71000 00:05 14797 /dev/nvidia0
7f12a1710000-7f12a1b12000 rw-s 61d0fd000 00:05 14797 /dev/nvidia0
7f12a1b12000-7f12a1b13000 rw-s dfee5000 00:05 14797 /dev/nvidia0
7f12a1b13000-7f12a1b14000 rw-s 619755000 00:05 14797 /dev/nvidia0
7f12a1b14000-7f12a1f16000 rw-s 38b1a9000 00:05 14797 /dev/nvidia0
7f12a1f16000-7f12a2318000 rw-s 57bd9a000 00:05 14797 /dev/nvidia0
7f12a2318000-7f12a2319000 ---p 00000000 00:00 0
7f12a2319000-7f12a2b19000 rwxp 00000000 00:00 0
7f12a2b19000-7f12a2b1a000 ---p 00000000 00:00 0
7f12a2b1a000-7f12a331a000 rwxp 00000000 00:00 0
7f12a331a000-7f12a331b000 ---p 00000000 00:00 0
7f12a331b000-7f12a3b1b000 rwxp 00000000 00:00 0
7f12a3b1b000-7f12a3b1c000 ---p 00000000 00:00 0
7f12a3b1c000-7f12a431c000 rwxp 00000000 00:00 0
7f12a431c000-7f12a431d000 ---p 00000000 00:00 0
7f12a431d000-7f12a4b1d000 rwxp 00000000 00:00 0
7f12a4b1d000-7f12a4b1e000 ---p 00000000 00:00 0
7f12a4b1e000-7f12a531e000 rwxp 00000000 00:00 0
7f12a531e000-7f12a531f000 ---p 00000000 00:00 0
7f12a531f000-7f12a5b1f000 rwxp 00000000 00:00 0
7f12a5b1f000-7f12a5c1f000 rw-p 00000000 00:00 0
7f12a5c1f000-7f12a5d1f000 rw-s 406423000 00:05 14797 /dev/nvidia0
7f12a5d1f000-7f12a5e1f000 rw-p 00000000 00:00 0
7f12a5e1f000-7f12a5f1f000 rw-s 579992000 00:05 14797 /dev/nvidia0
7f12a5f1f000-7f12a621f000 rw-p 00000000 00:00 0
7f12a621f000-7f12a631f000 rw-s 3ad9b2000 00:05 14797 /dev/nvidia0
7f12a631f000-7f12a641f000 rw-p 00000000 00:00 0
7f12a641f000-7f12a651f000 rw-s 58ef6c000 00:05 14797 /dev/nvidia0
7f12a651f000-7f12a661f000 rw-p 00000000 00:00 0
7f12a661f000-7f12a6620000 rw-s dfee3000 00:05 14797 /dev/nvidia0
7f12a6620000-7f12a6621000 rw-s 58ef66000 00:05 14797 /dev/nvidia0
7f12a6621000-7f12a6a23000 rw-s 6655d3000 00:05 14797 /dev/nvidia0
7f12a6a23000-7f12a6a24000 rw-s dfee2000 00:05 14797 /dev/nvidia0
7f12a6a24000-7f12a6a25000 rw-s 3bf4bf000 00:05 14797 /dev/nvidia0
7f12a6a25000-7f12a6e27000 rw-s 62bcaf000 00:05 14797 /dev/nvidia0
7f12a6e27000-7f12a7229000 rw-s 6638a3000 00:05 14797 /dev/nvidia0
7f12a7229000-7f12a742a000 rw-p 00000000 00:00 0
7f12a742a000-7f12a742b000 ---p 00000000 00:00 0
7f12a742b000-7f12a7c2b000 rwxp 00000000 00:00 0
7f12a7c2b000-7f12a8374000 r-xp 00000000 08:01 1063223 /usr/lib/libnvidia-opencl.so.304.54
7f12a8374000-7f12a8574000 ---p 00749000 08:01 1063223 /usr/lib/libnvidia-opencl.so.304.54
7f12a8574000-7f12a8665000 rw-p 00749000 08:01 1063223 /usr/lib/libnvidia-opencl.so.304.54
7f12a8665000-7f12a868b000 rw-p 00000000 00:00 0
7f12a868b000-7f12a871d000 r-xp 00000000 08:01 950791 /tmp/OpenMM5.1RC2-Build/libOpenMMAmoeba.so
7f12a871d000-7f12a891d000 ---p 00092000 08:01 950791 /tmp/OpenMM5.1RC2-Build/libOpenMMAmoeba.so
7f12a891d000-7f12a891f000 r--p 00092000 08:01 950791 /tmp/OpenMM5.1RC2-Build/libOpenMMAmoeba.so
7f12a891f000-7f12a8921000 rw-p 00094000 08:01 950791 /tmp/OpenMM5.1RC2-Build/libOpenMMAmoeba.so
7f12a8921000-7f12a89c0000 r-xp 00000000 08:01 44577 /usr/local/OpenMM5.0/lib/plugins/libOpenMMAmoebaCUDA.so
7f12a89c0000-7f12a8bc0000 ---p 0009f000 08:01 44577 /usr/local/OpenMM5.0/lib/plugins/libOpenMMAmoebaCUDA.so
7f12a8bc0000-7f12a8bc2000 r--p 0009f000 08:01 44577 /usr/local/OpenMM5.0/lib/plugins/libOpenMMAmoebaCUDA.so
7f12a8bc2000-7f12a8bc3000 rw-p 000a1000 08:01 44577 /usr/local/OpenMM5.0/lib/plugins/libOpenMMAmoebaCUDA.so
7f12a8bc3000-7f12a8bd7000 r-xp 00000000 08:01 44579 /usr/local/OpenMM5.0/lib/plugins/libOpenMMRPMDOpenCL.so
7f12a8bd7000-7f12a8dd6000 ---p 00014000 08:01 44579 /usr/local/OpenMM5.0/lib/plugins/libOpenMMRPMDOpenCL.so
7f12a8dd6000-7f12a8dd7000 r--p 00013000 08:01 44579 /usr/local/OpenMM5.0/lib/plugins/libOpenMMRPMDOpenCL.so
7f12a8dd7000-7f12a8dd8000 rw-p 00014000 08:01 44579 /usr/local/OpenMM5.0/lib/plugins/libOpenMMRPMDOpenCL.so
7f12a8dd8000-7f12a8f0a000 r-xp 00000000 08:01 44574 /usr/local/OpenMM5.0/lib/plugins/libOpenMMCUDA.so
7f12a8f0a000-7f12a9109000 ---p 00132000 08:01 44574 /usr/local/OpenMM5.0/lib/plugins/libOpenMMCUDA.so
7f12a9109000-7f12a910d000 r--p 00131000 08:01 44574 /usr/local/OpenMM5.0/lib/plugins/libOpenMMCUDA.so
7f12a910d000-7f12a910f000 rw-p 00135000 08:01 44574 /usr/local/OpenMM5.0/lib/plugins/libOpenMMCUDA.so
7f12a910f000-7f12a9167000 r-xp 00000000 08:01 1270723 /usr/local/cuda-5.0/lib64/libcudart.so.5.0.35
7f12a9167000-7f12a9367000 ---p 00058000 08:01 1270723 /usr/local/cuda-5.0/lib64/libcudart.so.5.0.35
7f12a9367000-7f12a9368000 r--p 00058000 08:01 1270723 /usr/local/cuda-5.0/lib64/libcudart.so.5.0.35
7f12a9368000-7f12a9369000 rw-p 00059000 08:01 1270723 /usr/local/cuda-5.0/lib64/libcudart.so.5.0.35
7f12a9369000-7f12aaf96000 r-xp 00000000 08:01 1270709 /usr/local/cuda-5.0/lib64/libcufft.so.5.0.35
7f12aaf96000-7f12ab195000 ---p 01c2d000 08:01 1270709 /usr/local/cuda-5.0/lib64/libcufft.so.5.0.35
7f12ab195000-7f12ab290000 r--p 01c2c000 08:01 1270709 /usr/local/cuda-5.0/lib64/libcufft.so.5.0.35
7f12ab290000-7f12ab29d000 rw-p 01d27000 08:01 1270709 /usr/local/cuda-5.0/lib64/libcufft.so.5.0.35
7f12ab29d000-7f12ab31f000 rw-p 00000000 00:00 0
7f12ab31f000-7f12ab326000 r-xp 00000000 08:01 303195 /lib/x86_64-linux-gnu/librt-2.15.so
7f12ab326000-7f12ab525000 ---p 00007000 08:01 303195 /lib/x86_64-linux-gnu/librt-2.15.so
7f12ab525000-7f12ab526000 r--p 00006000 08:01 303195 /lib/x86_64-linux-gnu/librt-2.15.so
7f12ab526000-7f12ab527000 rw-p 00007000 08:01 303195 /lib/x86_64-linux-gnu/librt-2.15.so
7f12ab527000-7f12ab53d000 r-xp 00000000 08:01 1308177 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f12ab53d000-7f12ab73c000 ---p 00016000 08:01 1308177 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f12ab73c000-7f12ab73d000 r--p 00015000 08:01 1308177 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f12ab73d000-7f12ab73e000 rw-p 00016000 08:01 1308177 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f12ab73e000-7f12ab87c000 r-xp 00000000 08:01 950445 /tmp/OpenMM5.1RC2-Build/libOpenMMCUDA.so
7f12ab87c000-7f12aba7c000 ---p 0013e000 08:01 950445 /tmp/OpenMM5.1RC2-Build/libOpenMMCUDA.so
7f12aba7c000-7f12aba80000 r--p 0013e000 08:01 950445 /tmp/OpenMM5.1RC2-Build/libOpenMMCUDA.so
7f12aba80000-7f12aba82000 rw-p 00142000 08:01 950445 /tmp/OpenMM5.1RC2-Build/libOpenMMCUDA.so
7f12aba82000-7f12ac32f000 r-xp 00000000 08:01 1063222 /usr/lib/libcuda.so.304.54
7f12ac32f000-7f12ac52e000 ---p 008ad000 08:01 1063222 /usr/lib/libcuda.so.304.54
7f12ac52e000-7f12ac640000 rw-p 008ac000 08:01 1063222 /usr/lib/libcuda.so.304.54
7f12ac640000-7f12ac669000 rw-p 00000000 00:00 0
7f12ac669000-7f12ac67b000 r-xp 00000000 08:01 44580 /usr/local/OpenMM5.0/lib/plugins/libOpenMMRPMDCUDA.so
7f12ac67b000-7f12ac87b000 ---p 00012000 08:01 44580 /usr/local/OpenMM5.0/lib/plugins/libOpenMMRPMDCUDA.so
7f12ac87b000-7f12ac87c000 r--p 00012000 08:01 44580 /usr/local/OpenMM5.0/lib/plugins/libOpenMMRPMDCUDA.so
7f12ac87c000-7f12ac87d000 rw-p 00013000 08:01 44580 /usr/local/OpenMM5.0/lib/plugins/libOpenMMRPMDCUDA.so
7f12ac87d000-7f12ac9db000 r-xp 00000000 08:01 44575 /usr/local/OpenMM5.0/lib/plugins/libOpenMMOpenCL.so
7f12ac9db000-7f12acbda000 ---p 0015e000 08:01 44575 /usr/local/OpenMM5.0/lib/plugins/libOpenMMOpenCL.so
7f12acbda000-7f12acbde000 r--p 0015d000 08:01 44575 /usr/local/OpenMM5.0/lib/plugins/libOpenMMOpenCL.so
7f12acbde000-7f12acbe0000 rw-p 00161000 08:01 44575 /usr/local/OpenMM5.0/lib/plugins/libOpenMMOpenCL.so
7f12acbe0000-7f12acbe2000 r-xp 00000000 08:01 1308412 /lib/x86_64-linux-gnu/libdl-2.15.so
7f12acbe2000-7f12acde2000 ---p 00002000 08:01 1308412 /lib/x86_64-linux-gnu/libdl-2.15.so
7f12acde2000-7f12acde3000 r--p 00002000 08:01 1308412 /lib/x86_64-linux-gnu/libdl-2.15.so
7f12acde3000-7f12acde4000 rw-p 00003000 08:01 1308412 /lib/x86_64-linux-gnu/libdl-2.15.so
7f12acde4000-7f12acdfc000 r-xp 00000000 08:01 302513 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f12acdfc000-7f12acffb000 ---p 00018000 08:01 302513 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f12acffb000-7f12acffc000 r--p 00017000 08:01 302513 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f12acffc000-7f12acffd000 rw-p 00018000 08:01 302513 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f12acffd000-7f12ad001000 rw-p 00000000 00:00 0
7f12ad001000-7f12ad005000 r-xp 00000000 08:01 1063224 /usr/lib/libOpenCL.so.1.0.0
7f12ad005000-7f12ad205000 ---p 00004000 08:01 1063224 /usr/lib/libOpenCL.so.1.0.0
7f12ad205000-7f12ad206000 rw-p 00004000 08:01 1063224 /usr/lib/libOpenCL.so.1.0.0
7f12ad206000-7f12ad3bb000 r-xp 00000000 08:01 1308413 /lib/x86_64-linux-gnu/libc-2.15.so
7f12ad3bb000-7f12ad5ba000 ---p 001b5000 08:01 1308413 /lib/x86_64-linux-gnu/libc-2.15.so
7f12ad5ba000-7f12ad5be000 r--p 001b4000 08:01 1308413 /lib/x86_64-linux-gnu/libc-2.15.so
7f12ad5be000-7f12ad5c0000 rw-p 001b8000 08:01 1308413 /lib/x86_64-linux-gnu/libc-2.15.so
7f12ad5c0000-7f12ad5c5000 rw-p 00000000 00:00 0
7f12ad5c5000-7f12ad5da000 r-xp 00000000 08:01 1308187 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f12ad5da000-7f12ad7d9000 ---p 00015000 08:01 1308187 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f12ad7d9000-7f12ad7da000 r--p 00014000 08:01 1308187 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f12ad7da000-7f12ad7db000 rw-p 00015000 08:01 1308187 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f12ad7db000-7f12ad8d6000 r-xp 00000000 08:01 303341 /lib/x86_64-linux-gnu/libm-2.15.so
7f12ad8d6000-7f12adad5000 ---p 000fb000 08:01 303341 /lib/x86_64-linux-gnu/libm-2.15.so
7f12adad5000-7f12adad6000 r--p 000fa000 08:01 303341 /lib/x86_64-linux-gnu/libm-2.15.so
7f12adad6000-7f12adad7000 rw-p 000fb000 08:01 303341 /lib/x86_64-linux-gnu/libm-2.15.so
7f12adad7000-7f12adbb9000 r-xp 00000000 08:01 1071644 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f12adbb9000-7f12addb8000 ---p 000e2000 08:01 1071644 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f12addb8000-7f12addc0000 r--p 000e1000 08:01 1071644 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f12addc0000-7f12addc2000 rw-p 000e9000 08:01 1071644 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f12addc2000-7f12addd7000 rw-p 00000000 00:00 0
7f12addd7000-7f12adf40000 r-xp 00000000 08:01 950292 /tmp/OpenMM5.1RC2-Build/libOpenMM.so
7f12adf40000-7f12ae140000 ---p 00169000 08:01 950292 /tmp/OpenMM5.1RC2-Build/libOpenMM.so
7f12ae140000-7f12ae146000 r--p 00169000 08:01 950292 /tmp/OpenMM5.1RC2-Build/libOpenMM.so
7f12ae146000-7f12ae148000 rw-p 0016f000 08:01 950292 /tmp/OpenMM5.1RC2-Build/libOpenMM.so
7f12ae148000-7f12ae149000 rw-p 00000000 00:00 0
7f12ae149000-7f12ae2b2000 r-xp 00000000 08:01 950602 /tmp/OpenMM5.1RC2-Build/libOpenMMOpenCL.so
7f12ae2b2000-7f12ae4b1000 ---p 00169000 08:01 950602 /tmp/OpenMM5.1RC2-Build/libOpenMMOpenCL.so
7f12ae4b1000-7f12ae4b5000 r--p 00168000 08:01 950602 /tmp/OpenMM5.1RC2-Build/libOpenMMOpenCL.so
7f12ae4b5000-7f12ae4b7000 rw-p 0016c000 08:01 950602 /tmp/OpenMM5.1RC2-Build/libOpenMMOpenCL.so
7f12ae4b7000-7f12ae4d9000 r-xp 00000000 08:01 303347 /lib/x86_64-linux-gnu/ld-2.15.so
7f12ae5aa000-7f12ae6b1000 rw-p 00000000 00:00 0
7f12ae6c8000-7f12ae6c9000 rw-p 00000000 00:00 0
7f12ae6c9000-7f12ae6ca000 rw-s dfee9000 00:05 14797 /dev/nvidia0
7f12ae6ca000-7f12ae6cb000 rw-s 5799bd000 00:05 14797 /dev/nvidia0
7f12ae6cb000-7f12ae6cc000 rw-s dfee8000 00:05 14797 /dev/nvidia0
7f12ae6cc000-7f12ae6cd000 rw-s 59d095000 00:05 14797 /dev/nvidia0
7f12ae6cd000-7f12ae6ce000 rw-s dfee7000 00:05 14797 /dev/nvidia0
7f12ae6ce000-7f12ae6cf000 rw-s 3d5c21000 00:05 14797 /dev/nvidia0
7f12ae6cf000-7f12ae6d0000 rw-s dfee4000 00:05 14797 /dev/nvidia0
7f12ae6d0000-7f12ae6d1000 rw-s 54ef29000 00:05 14797 /dev/nvidia0
7f12ae6d1000-7f12ae6d2000 rw-s dfee1000 00:05 14797 /dev/nvidia0
7f12ae6d2000-7f12ae6d3000 r--s d5009000 00:05 19680 /dev/nvidia2
7f12ae6d3000-7f12ae6d4000 r--s d3009000 00:05 11855 /dev/nvidia1
7f12ae6d4000-7f12ae6d5000 r--s f9009000 00:05 14797 /dev/nvidia0
7f12ae6d5000-7f12ae6d6000 rw-s 3ae827000 00:05 14797 /dev/nvidia0
7f12ae6d6000-7f12ae6d9000 rw-p 00000000 00:00 0
7f12ae6d9000-7f12ae6da000 r--p 00022000 08:01 303347 /lib/x86_64-linux-gnu/ld-2.15.so
7f12ae6da000-7f12ae6dc000 rw-p 00023000 08:01 303347 /lib/x86_64-linux-gnu/ld-2.15.so
7fff8917c000-7fff8919d000 rwxp 00000000 00:00 0 [stack]
7fff891ff000-7fff89200000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)

Clearing these environment settings and repeating, does not trigger the issue:

<comment out from .bashrc and logout/login
#export OPENMM_HOME=/usr/local/OpenMM5.0
#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$OPENMM_HOME/lib:$OPENMM_HOME/lib/plugins
#export OPENMM_PLUGIN_DIR=$OPENMM_HOME/lib/plugins
>

$ ./TestOpenCLNonbondedForce2
Done



As I said, this is fundamentally a user bug; I am accidentally using older OpenMM environment variables (hence linking to older libs), however, it is my understanding that all the tests in the Build directory should be relative to what has been build in *that* directory and not what is installed elsewhere on the system. As I said, this is subjective, but resolving this could prevent false bugs from being reported in future.

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