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hainm/test_sanderapi_log.02052017.BAD.txt

Created February 5, 2017 06:03
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  1. hainm created this gist Feb 5, 2017.
    252 changes: 252 additions & 0 deletions test_sanderapi_log.02052017.BAD.txt
    View file
    Original file line number Diff line number Diff line change
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    amber/test/sanderapi ((no branch, rebasing master)) $ make
    make[1]: Entering directory `/net/casegroupp/u1/haichit/amber_git/amber/test/sanderapi'
    Creating the bad prmtop test.parm7
    Testing the Fortran API
    gfortran -I/home/haichit/amber_git/amber/include -L/home/haichit/amber_git/amber/lib test.F90 -o testf -lsander
    Running testf
    Checking proper treatment of a bad prmtop
    ERROR: Flag "ATOM_NAME" not found in PARM file
    PASSED
    ==============================================================
    Checking proper treatment of bad input

    unreasonably small cut for non-periodic run: 1.00
    PASSED
    ==============================================================
    Testing GB sander interface
    PASSED
    ==============================================================
    Testing PME sander interface
    PASSED
    ==============================================================
    Testing the QM/MM non-periodic interface
    PASSED
    ==============================================================
    Testing the QM/MM periodic interface (PM3-PDDG)
    PASSED
    ==============================================================
    Testing the QM/MM periodic interface (DFTB)
    Could not find the SLKO files. Skipping this test.
    ==============================================================
    Testing the broader API functionality
    PASSED
    ==============================================================
    Checking get_positions call
    PASSED
    ==============================================================
    Testing the Fortran file-less API
    gfortran -I/home/haichit/amber_git/amber/include -L/home/haichit/amber_git/amber/lib test2.F90 -o testf2 -lsander
    Running testf2
    Testing GB sander interface
    PASSED
    ==============================================================
    Testing PME sander interface
    PASSED
    ==============================================================
    Testing the QM/MM non-periodic interface
    PASSED
    ==============================================================
    Testing the QM/MM periodic interface (PM3-PDDG)
    PASSED
    ==============================================================
    Testing the C API
    /home/haichit/programs/gcc61/install//bin/gcc -I/home/haichit/amber_git/amber/include -L/home/haichit/amber_git/amber/lib test.c -o testc -lsander
    Running testc
    Testing proper treatment of a bad prmtop
    ERROR: Flag "ATOM_NAME" not found in PARM file
    PASSED
    ==============================================================
    Testing proper treatment of bad input

    unreasonably small cut for non-periodic run: 5.00
    PASSED
    ==============================================================
    Testing GB sander interface
    PASSED
    ==============================================================
    Testing PME sander interface
    PASSED
    ==============================================================
    Testing the QM/MM non-periodic interface
    QMMM is not compatible with Poisson Boltzmann (igb=10 or ipb/=0).

    Bond failed: Expected 0.0016 got 0.0000
    Angle failed: Expected 0.3736 got 0.0000
    Dihedral failed: Expected 0.0026 got 0.0000
    1-4 vdW failed: Expected 3.7051 got 0.0000
    1-4 Elec failed: Expected 65.9137 got 0.0000
    van der Waals failed: Expected 0.1908 got 0.0000
    Electrostatic failed: Expected -4.1241 got 0.0000
    EGB failed: Expected -80.1406 got 0.0000
    QM Escf failed: Expected -11.9100 got 0.0000
    Possible FAILURE
    ==============================================================
    *** glibc detected *** ./testc: free(): invalid next size (fast): 0x000000000e8c4ad0 ***
    *** glibc detected *** ./testc: malloc(): memory corruption: 0x000000000e8c4af0 ***
    ======= Backtrace: =========
    /lib64/libc.so.6[0x3093a71fbe]
    /lib64/libc.so.6(__libc_malloc+0x6e)[0x3093a73dfe]
    /lib64/ld-linux-x86-64.so.2[0x309360bbab]
    /lib64/ld-linux-x86-64.so.2[0x3093610f02]
    /lib64/ld-linux-x86-64.so.2[0x309360d136]
    /lib64/ld-linux-x86-64.so.2[0x30936108bc]
    /lib64/libc.so.6[0x3093b0a000]
    /lib64/ld-linux-x86-64.so.2[0x309360d136]
    /lib64/libc.so.6(__libc_dlopen_mode+0x47)[0x3093b0a167]
    /lib64/libc.so.6(backtrace+0x9f)[0x3093ae73af]
    /lib64/libc.so.6[0x3093a6995f]
    /lib64/libc.so.6[0x3093a714af]
    /lib64/libc.so.6(cfree+0x4b)[0x3093a757ab]
    ./testc[0x401a29]
    /lib64/libc.so.6(__libc_start_main+0xf4)[0x3093a1d9f4]
    ./testc[0x400c79]
    ======= Memory map: ========
    00400000-00404000 r-xp 00000000 00:34 161023905 /net/casegroupp/u1/haichit/amber_git/amber/test/sanderapi/testc
    00603000-00604000 rw-p 00003000 00:34 161023905 /net/casegroupp/u1/haichit/amber_git/amber/test/sanderapi/testc
    0e86c000-0f186000 rw-p 0e86c000 00:00 0 [heap]
    3093600000-309361c000 r-xp 00000000 08:01 6142622 /lib64/ld-2.5.so
    309381c000-309381d000 r--p 0001c000 08:01 6142622 /lib64/ld-2.5.so
    309381d000-309381e000 rw-p 0001d000 08:01 6142622 /lib64/ld-2.5.so
    3093a00000-3093b4f000 r-xp 00000000 08:01 6142866 /lib64/libc-2.5.so
    3093b4f000-3093d4f000 ---p 0014f000 08:01 6142866 /lib64/libc-2.5.so
    3093d4f000-3093d53000 r--p 0014f000 08:01 6142866 /lib64/libc-2.5.so
    3093d53000-3093d54000 rw-p 00153000 08:01 6142866 /lib64/libc-2.5.so
    3093d54000-3093d59000 rw-p 3093d54000 00:00 0
    3093e00000-3093e82000 r-xp 00000000 08:01 6142869 /lib64/libm-2.5.so
    3093e82000-3094081000 ---p 00082000 08:01 6142869 /lib64/libm-2.5.so
    3094081000-3094082000 r--p 00081000 08:01 6142869 /lib64/libm-2.5.so
    3094082000-3094083000 rw-p 00082000 08:01 6142869 /lib64/libm-2.5.so
    3094200000-3094202000 r-xp 00000000 08:01 6142870 /lib64/libdl-2.5.so
    3094202000-3094402000 ---p 00002000 08:01 6142870 /lib64/libdl-2.5.so
    3094402000-3094403000 r--p 00002000 08:01 6142870 /lib64/libdl-2.5.so
    3094403000-3094404000 rw-p 00003000 08:01 6142870 /lib64/libdl-2.5.so
    2ba681cd5000-2ba681cd7000 rw-p 2ba681cd5000 00:00 0
    2ba681cd7000-2ba6826ec000 r-xp 00000000 00:34 161057593 /net/casegroupp/u1/haichit/amber_git/amber/lib/libsander.so
    2ba6826ec000-2ba6828ec000 ---p 00a15000 00:34 161057593 /net/casegroupp/u1/haichit/amber_git/amber/lib/libsander.so
    2ba6828ec000-2ba682a0c000 rw-p 00a15000 00:34 161057593 /net/casegroupp/u1/haichit/amber_git/amber/lib/libsander.so
    2ba682a0c000-2ba697244000 rw-p 2ba682a0c000 00:00 0
    2ba697276000-2ba697277000 rw-p 2ba697276000 00:00 0
    2ba697277000-2ba697412000 r-xp 00000000 00:34 181896580 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libstdc++.so.6.0.22
    2ba697412000-2ba697612000 ---p 0019b000 00:34 181896580 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libstdc++.so.6.0.22
    2ba697612000-2ba69761c000 r--p 0019b000 00:34 181896580 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libstdc++.so.6.0.22
    2ba69761c000-2ba69761e000 rw-p 001a5000 00:34 181896580 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libstdc++.so.6.0.22
    2ba69761e000-2ba697622000 rw-p 2ba69761e000 00:00 0
    2ba697622000-2ba697754000 r-xp 00000000 00:34 181896676 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgfortran.so.3.0.0
    2ba697754000-2ba697954000 ---p 00132000 00:34 181896676 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgfortran.so.3.0.0
    2ba697954000-2ba697956000 rw-p 00132000 00:34 181896676 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgfortran.so.3.0.0
    2ba697956000-2ba697957000 rw-p 2ba697956000 00:00 0
    2ba697957000-2ba69796d000 r-xp 00000000 00:34 181895787 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgcc_s.so.1
    2ba69796d000-2ba697b6d000 ---p 00016000 00:34 181895787 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgcc_s.so.1
    2ba697b6d000-2ba697b6e000 rw-p 00016000 00:34 181895787 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgcc_s.so.1
    2ba697b6e000-2ba697bad000 r-xp 00000000 00:34 181896666 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libquadmath.so.0.0.0
    2ba697bad000-2ba697dad000 ---p 0003f000 00:34 181896666 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libquadmath.so.0.0.0
    2ba697dad000-2ba697dae000 rw-p 0003f000 00:34 181896666 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libquadmath.so.0.0.0
    2ba697dae000-2ba697db1000 rw-p 2ba697dae000 00:00 0
    2ba698000000-2ba698021000 rw-p 2ba698000000 00:00 0
    2ba698021000-2ba69c000000 ---p 2ba698021000 00:00 0
    7fff755ba000-7fff7560b000 rw-p 7ffffffad000 00:00 0 [stack]
    7fff757ae000-7fff757b1000 r-xp 7fff757ae000 00:00 0 [vdso]
    ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vsyscall]
    /bin/sh: line 1: 1234 Aborted ./testc
    Program error
    Testing the C++ API
    /home/haichit/programs/gcc61/install//bin/g++ -I/home/haichit/amber_git/amber/include -L/home/haichit/amber_git/amber/lib test.cpp -o testcpp -lsander
    Running testcpp
    Testing GB sander interface
    PASSED
    ==============================================================
    Testing PME sander interface
    PASSED
    ==============================================================
    Checking for consistent forces
    PASSED
    ==============================================================
    Testing the QM/MM non-periodic interface
    QMMM is not compatible with Poisson Boltzmann (igb=10 or ipb/=0).

    Bond failed: Expected 0.0016 got 0.0000
    Angle failed: Expected 0.3736 got 0.0000
    Dihedral failed: Expected 0.0026 got 0.0000
    1-4 vdW failed: Expected 3.7051 got 0.0000
    1-4 Elec failed: Expected 65.9137 got 0.0000
    van der Waals failed: Expected 0.1908 got 0.0000
    Electrostatic failed: Expected -4.1241 got 0.0000
    EGB failed: Expected -80.1406 got 0.0000
    QM Escf failed: Expected -11.9100 got 0.0000
    Possible FAILURE
    ==============================================================
    *** glibc detected *** ./testcpp: free(): invalid next size (fast): 0x00000000129e4190 ***
    *** glibc detected *** ./testcpp: malloc(): memory corruption: 0x00000000129e5770 ***
    ======= Backtrace: =========
    /lib64/libc.so.6[0x3093a71fbe]
    /lib64/libc.so.6(__libc_malloc+0x6e)[0x3093a73dfe]
    /lib64/ld-linux-x86-64.so.2[0x309360bbab]
    /lib64/ld-linux-x86-64.so.2[0x3093610f02]
    /lib64/ld-linux-x86-64.so.2[0x309360d136]
    /lib64/ld-linux-x86-64.so.2[0x30936108bc]
    /lib64/libc.so.6[0x3093b0a000]
    /lib64/ld-linux-x86-64.so.2[0x309360d136]
    /lib64/libc.so.6(__libc_dlopen_mode+0x47)[0x3093b0a167]
    /lib64/libc.so.6(backtrace+0x9f)[0x3093ae73af]
    /lib64/libc.so.6[0x3093a6995f]
    /lib64/libc.so.6[0x3093a714af]
    /lib64/libc.so.6(cfree+0x4b)[0x3093a757ab]
    ./testcpp[0x4027d7]
    /lib64/libc.so.6(__libc_start_main+0xf4)[0x3093a1d9f4]
    ./testcpp(_ZNSt8ios_base4InitD1Ev+0x41)[0x4015b9]
    ======= Memory map: ========
    00400000-00405000 r-xp 00000000 00:34 161023906 /net/casegroupp/u1/haichit/amber_git/amber/test/sanderapi/testcpp
    00605000-00606000 rw-p 00005000 00:34 161023906 /net/casegroupp/u1/haichit/amber_git/amber/test/sanderapi/testcpp
    1298d000-132a3000 rw-p 1298d000 00:00 0 [heap]
    3093600000-309361c000 r-xp 00000000 08:01 6142622 /lib64/ld-2.5.so
    309381c000-309381d000 r--p 0001c000 08:01 6142622 /lib64/ld-2.5.so
    309381d000-309381e000 rw-p 0001d000 08:01 6142622 /lib64/ld-2.5.so
    3093a00000-3093b4f000 r-xp 00000000 08:01 6142866 /lib64/libc-2.5.so
    3093b4f000-3093d4f000 ---p 0014f000 08:01 6142866 /lib64/libc-2.5.so
    3093d4f000-3093d53000 r--p 0014f000 08:01 6142866 /lib64/libc-2.5.so
    3093d53000-3093d54000 rw-p 00153000 08:01 6142866 /lib64/libc-2.5.so
    3093d54000-3093d59000 rw-p 3093d54000 00:00 0
    3093e00000-3093e82000 r-xp 00000000 08:01 6142869 /lib64/libm-2.5.so
    3093e82000-3094081000 ---p 00082000 08:01 6142869 /lib64/libm-2.5.so
    3094081000-3094082000 r--p 00081000 08:01 6142869 /lib64/libm-2.5.so
    3094082000-3094083000 rw-p 00082000 08:01 6142869 /lib64/libm-2.5.so
    3094200000-3094202000 r-xp 00000000 08:01 6142870 /lib64/libdl-2.5.so
    3094202000-3094402000 ---p 00002000 08:01 6142870 /lib64/libdl-2.5.so
    3094402000-3094403000 r--p 00002000 08:01 6142870 /lib64/libdl-2.5.so
    3094403000-3094404000 rw-p 00003000 08:01 6142870 /lib64/libdl-2.5.so
    2ac06bf97000-2ac06bf99000 rw-p 2ac06bf97000 00:00 0
    2ac06bf99000-2ac06c9ae000 r-xp 00000000 00:34 161057593 /net/casegroupp/u1/haichit/amber_git/amber/lib/libsander.so
    2ac06c9ae000-2ac06cbae000 ---p 00a15000 00:34 161057593 /net/casegroupp/u1/haichit/amber_git/amber/lib/libsander.so
    2ac06cbae000-2ac06ccce000 rw-p 00a15000 00:34 161057593 /net/casegroupp/u1/haichit/amber_git/amber/lib/libsander.so
    2ac06ccce000-2ac081505000 rw-p 2ac06ccce000 00:00 0
    2ac081505000-2ac0816a0000 r-xp 00000000 00:34 181896580 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libstdc++.so.6.0.22
    2ac0816a0000-2ac0818a0000 ---p 0019b000 00:34 181896580 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libstdc++.so.6.0.22
    2ac0818a0000-2ac0818aa000 r--p 0019b000 00:34 181896580 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libstdc++.so.6.0.22
    2ac0818aa000-2ac0818ac000 rw-p 001a5000 00:34 181896580 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libstdc++.so.6.0.22
    2ac0818ac000-2ac0818b1000 rw-p 2ac0818ac000 00:00 0
    2ac0818e3000-2ac0818e4000 rw-p 2ac0818e3000 00:00 0
    2ac0818e4000-2ac0818fa000 r-xp 00000000 00:34 181895787 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgcc_s.so.1
    2ac0818fa000-2ac081afa000 ---p 00016000 00:34 181895787 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgcc_s.so.1
    2ac081afa000-2ac081afb000 rw-p 00016000 00:34 181895787 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgcc_s.so.1
    2ac081afb000-2ac081afc000 rw-p 2ac081afb000 00:00 0
    2ac081afc000-2ac081c2e000 r-xp 00000000 00:34 181896676 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgfortran.so.3.0.0
    2ac081c2e000-2ac081e2e000 ---p 00132000 00:34 181896676 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgfortran.so.3.0.0
    2ac081e2e000-2ac081e30000 rw-p 00132000 00:34 181896676 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libgfortran.so.3.0.0
    2ac081e30000-2ac081e6f000 r-xp 00000000 00:34 181896666 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libquadmath.so.0.0.0
    2ac081e6f000-2ac08206f000 ---p 0003f000 00:34 181896666 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libquadmath.so.0.0.0
    2ac08206f000-2ac082070000 rw-p 0003f000 00:34 181896666 /net/casegroupp/u1/haichit/programs/gcc61/install/lib64/libquadmath.so.0.0.0
    2ac082070000-2ac082073000 rw-p 2ac082070000 00:00 0
    2ac084000000-2ac084021000 rw-p 2ac084000000 00:00 0
    2ac084021000-2ac088000000 ---p 2ac084021000 00:00 0
    7fff4ebbf000-7fff4ec0e000 rw-p 7ffffffaf000 00:00 0 [stack]
    7fff4ec1a000-7fff4ec1d000 r-xp 7fff4ec1a000 00:00 0 [vdso]
    ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vsyscall]
    /bin/sh: line 1: 1250 Aborted ./testcpp
    Program error
    Testing the Python API
    /home/haichit/miniconda3/bin/python test.py
    Testing GB sander interface
    /bin/sh: line 1: 1254 Segmentation fault /home/haichit/miniconda3/bin/python test.py
    Program error
    /bin/rm -f test.parm7 testf testf2 testc testcpp
    make[1]: Leaving directory `/net/casegroupp/u1/haichit/amber_git/amber/test/sanderapi'