+ env
+ sort
 [ $? = 0 ] && eval $(${LMOD_SETTARG_CMD:-:} -s sh)
AMBER=/mnt/storage/software/apps/Amber18-MPI/amber18/bin/pmemd.cuda
AMBERHOME=/mnt/storage/software/apps/Amber18-MPI/amber18
AMBERPREFIX=/mnt/storage/software/apps/Amber18-MPI/amber18
BASH_ENV=/usr/share/lmod/lmod/init/bash
BASH_FUNC_ml()=() {  eval $($LMOD_DIR/ml_cmd "$@")
BASH_FUNC_module()=() {  eval $($LMOD_CMD bash "$@");
CONDA_DEFAULT_ENV=westpa-2.0
CONDA_EXE=/mnt/storage/scratch/ft18983/miniconda3/bin/conda
CONDA_PREFIX=/mnt/storage/scratch/ft18983/miniconda3/envs/westpa-2.0
CONDA_PREFIX_1=/mnt/storage/scratch/ft18983/miniconda3
CONDA_PROMPT_MODIFIER=(westpa-2.0) 
CONDA_PYTHON_EXE=/mnt/storage/scratch/ft18983/miniconda3/bin/python
CONDA_SHLVL=2
CPATH=/mnt/storage/easybuild/software/OpenMPI/2.0.2-GCC-6.3.0-2.27/include:/mnt/storage/easybuild/software/hwloc/1.11.5-GCC-6.3.0-2.27/include:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-6.3.0-2.27/include:/mnt/storage/easybuild/software/binutils/2.27-GCCcore-6.3.0/include:/mnt/storage/easybuild/software/GCCcore/6.3.0/include:/mnt/storage/software/libraries/nvidia/cuda-9.0/include
CPLUS_INCLUDE_PATH=/mnt/storage/home/ft18983/local/plumed-2.5.2/include:
CPPTRAJ=/mnt/storage/software/apps/Amber18-MPI/amber18/bin/cpptraj
CUDA_HOME=/mnt/storage/software/libraries/nvidia/cuda-9.0
CUDA_PATH=/mnt/storage/software/libraries/nvidia/cuda-9.0
CUDA_VISIBLE_DEVICES=0
CVS_RSH=ssh
C_INCLUDE_PATH=/mnt/storage/home/ft18983/local/plumed-2.5.2/include:
EBDEVELBINUTILS=/mnt/storage/easybuild/software/binutils/2.27-GCCcore-6.3.0/easybuild/binutils-2.27-GCCcore-6.3.0-easybuild-devel
EBDEVELGCC=/mnt/storage/easybuild/software/GCC/6.3.0-2.27/easybuild/GCC-6.3.0-2.27-easybuild-devel
EBDEVELGCCCORE=/mnt/storage/easybuild/software/GCCcore/6.3.0/easybuild/GCCcore-6.3.0-easybuild-devel
EBDEVELHWLOC=/mnt/storage/easybuild/software/hwloc/1.11.5-GCC-6.3.0-2.27/easybuild/hwloc-1.11.5-GCC-6.3.0-2.27-easybuild-devel
EBDEVELNUMACTL=/mnt/storage/easybuild/software/numactl/2.0.11-GCC-6.3.0-2.27/easybuild/numactl-2.0.11-GCC-6.3.0-2.27-easybuild-devel
EBDEVELOPENMPI=/mnt/storage/easybuild/software/OpenMPI/2.0.2-GCC-6.3.0-2.27/easybuild/OpenMPI-2.0.2-GCC-6.3.0-2.27-easybuild-devel
EBROOTBINUTILS=/mnt/storage/easybuild/software/binutils/2.27-GCCcore-6.3.0
EBROOTGCC=/mnt/storage/easybuild/software/GCCcore/6.3.0
EBROOTGCCCORE=/mnt/storage/easybuild/software/GCCcore/6.3.0
EBROOTHWLOC=/mnt/storage/easybuild/software/hwloc/1.11.5-GCC-6.3.0-2.27
EBROOTNUMACTL=/mnt/storage/easybuild/software/numactl/2.0.11-GCC-6.3.0-2.27
EBROOTOPENMPI=/mnt/storage/easybuild/software/OpenMPI/2.0.2-GCC-6.3.0-2.27
EBVERSIONBINUTILS=2.27
EBVERSIONGCC=6.3.0
EBVERSIONGCCCORE=6.3.0
EBVERSIONHWLOC=1.11.5
EBVERSIONNUMACTL=2.0.11
EBVERSIONOPENMPI=2.0.2
ENVIRONMENT=BATCH
GMXBIN=/mnt/storage/home/ft18983/local/gromacs-2019.2/bin
GMXDATA=/mnt/storage/home/ft18983/local/gromacs-2019.2/share/gromacs
GMXLDLIB=/mnt/storage/home/ft18983/local/gromacs-2019.2/lib64
GMXMAN=/mnt/storage/home/ft18983/local/gromacs-2019.2/share/man
GPU_DEVICE_ORDINAL=0
GROMACS_DIR=/mnt/storage/home/ft18983/local/gromacs-2019.2
GSETTINGS_SCHEMA_DIR=/mnt/storage/scratch/ft18983/miniconda3/envs/westpa-2.0/share/glib-2.0/schemas
GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
HISTCONTROL=ignoredups
HISTIGNORE=opaswitchadmin*:opasaquery*:opaswquery*
HISTSIZE=1000
HOME=/mnt/storage/home/ft18983
HOSTNAME=gpu31
LANG=en_US.UTF-8
LC_ALL=POSIX
LC_CTYPE=POSIX
LD_LIBRARY_PATH=/mnt/storage/software/apps/Amber18-MPI/amber18/lib:/mnt/storage/easybuild/software/OpenMPI/2.0.2-GCC-6.3.0-2.27/lib:/mnt/storage/easybuild/software/hwloc/1.11.5-GCC-6.3.0-2.27/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-6.3.0-2.27/lib:/mnt/storage/easybuild/software/binutils/2.27-GCCcore-6.3.0/lib:/mnt/storage/easybuild/software/GCCcore/6.3.0/lib/gcc/x86_64-pc-linux-gnu/6.3.0:/mnt/storage/easybuild/software/GCCcore/6.3.0/lib64:/mnt/storage/easybuild/software/GCCcore/6.3.0/lib:/mnt/storage/software/libraries/nvidia/cudnn-9.0/cuda/lib64:/mnt/storage/software/libraries/nvidia/cuda-9.0/lib64:/mnt/storage/home/ft18983/local/plumed-2.5.2/lib:/mnt/storage/home/ft18983/local/gromacs-2019.2/lib64
LESSOPEN=||/usr/bin/lesspipe.sh %s
LIBRARY_PATH=/mnt/storage/easybuild/software/OpenMPI/2.0.2-GCC-6.3.0-2.27/lib:/mnt/storage/easybuild/software/hwloc/1.11.5-GCC-6.3.0-2.27/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-6.3.0-2.27/lib:/mnt/storage/easybuild/software/binutils/2.27-GCCcore-6.3.0/lib:/mnt/storage/easybuild/software/GCCcore/6.3.0/lib64:/mnt/storage/easybuild/software/GCCcore/6.3.0/lib:/mnt/storage/software/libraries/nvidia/cuda-9.0/lib64:/mnt/storage/software/libraries/nvidia/cudnn-9.0/cuda/lib64
LMOD_CMD=/usr/share/lmod/lmod/libexec/lmod
LMOD_COLORIZE=yes
LMOD_DEFAULT_MODULEPATH=/mnt/storage/easybuild/modules/local:/mnt/storage/easybuild/modules/all:/etc/modulefiles:/usr/share/modulefiles:/usr/share/Modules/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core
LMOD_DIR=/usr/share/lmod/lmod/libexec
LMOD_FULL_SETTARG_SUPPORT=no
LMOD_PKG=/usr/share/lmod/lmod
LMOD_PREPEND_BLOCK=normal
LMOD_SETTARG_CMD=:
LMOD_VERSION=6.5.1
LMOD_arch=x86_64
LMOD_sys=Linux
LOADEDMODULES=libs/cuda/9.0-gcc-5.4.0-2.26:libs/cudnn/9.0-cuda-9.0:GCCcore/6.3.0:binutils/2.27-GCCcore-6.3.0:GCC/6.3.0-2.27:numactl/2.0.11-GCC-6.3.0-2.27:hwloc/1.11.5-GCC-6.3.0-2.27:OpenMPI/2.0.2-GCC-6.3.0-2.27:apps/amber18/tools19-cuda-mpi-gnu-6.3.0
LOGNAME=ft18983
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:
MAIL=/var/spool/mail/ft18983
MANPATH=/mnt/storage/easybuild/software/OpenMPI/2.0.2-GCC-6.3.0-2.27/share/man:/mnt/storage/easybuild/software/hwloc/1.11.5-GCC-6.3.0-2.27/share/man:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-6.3.0-2.27/share/man:/mnt/storage/easybuild/software/binutils/2.27-GCCcore-6.3.0/share/man:/mnt/storage/easybuild/software/GCCcore/6.3.0/share/man:/mnt/storage/home/ft18983/local/gromacs-2019.2/share/man:/usr/share/lmod/lmod/share/man:/usr/local/share/man:/usr/share/man:/opt/ddn/ime/share/man:/opt/ddn/ime/share/man
MODULEPATH=/mnt/storage/easybuild/modules/local:/mnt/storage/easybuild/modules/all:/etc/modulefiles:/usr/share/modulefiles:/usr/share/Modules/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core
MODULEPATH_ROOT=/usr/share/modulefiles
MODULESHOME=/usr/share/lmod/lmod
NO_AT_BRIDGE=1
PATH=/mnt/storage/software/apps/Amber18-MPI/amber18/bin:/mnt/storage/easybuild/software/OpenMPI/2.0.2-GCC-6.3.0-2.27/bin:/mnt/storage/easybuild/software/hwloc/1.11.5-GCC-6.3.0-2.27/sbin:/mnt/storage/easybuild/software/hwloc/1.11.5-GCC-6.3.0-2.27/bin:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-6.3.0-2.27/bin:/mnt/storage/easybuild/software/binutils/2.27-GCCcore-6.3.0/bin:/mnt/storage/easybuild/software/GCCcore/6.3.0/bin:/mnt/storage/software/libraries/nvidia/cuda-9.0:/mnt/storage/software/libraries/nvidia/cuda-9.0/bin:/mnt/storage/scratch/ft18983/miniconda3/envs/westpa-2.0/bin:/mnt/storage/scratch/ft18983/miniconda3/condabin:/mnt/storage/home/ft18983/local/plumed-2.5.2/bin:/mnt/storage/home/ft18983/local/gromacs-2019.2/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/mnt/storage/home/ft18983/.dotnet/tools:/usr/lpp/mmfs/bin:/opt/ddn/ime/bin:/mnt/storage/home/ft18983/.local/bin:/mnt/storage/home/ft18983/bin
PKG_CONFIG_PATH=/mnt/storage/easybuild/software/OpenMPI/2.0.2-GCC-6.3.0-2.27/lib/pkgconfig:/mnt/storage/easybuild/software/hwloc/1.11.5-GCC-6.3.0-2.27/lib/pkgconfig:/mnt/storage/home/ft18983/local/plumed-2.5.2/lib/pkgconfig:/mnt/storage/home/ft18983/local/gromacs-2019.2/lib64/pkgconfig
PLUMED_KERNEL=/mnt/storage/home/ft18983/local/plumed-2.5.2/lib/libplumedKernel.so
PROPAGATION_DEBUG=1
PWD=/mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE
PYTHONPATH=:/mnt/storage/home/ft18983/scratch/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE
QT_GRAPHICSSYSTEM_CHECKED=1
SEG_DEBUG=1
SHELL=/bin/bash
SHLVL=3
SIM_NAME=ChemDyME_NA_OSE
SLURMD_NODENAME=gpu31
SLURM_CHECKPOINT_IMAGE_DIR=/var/slurm/checkpoint
SLURM_CLUSTER_NAME=bristol_cluster
SLURM_CPUS_ON_NODE=12
SLURM_GTIDS=0
SLURM_JOBID=5042618
SLURM_JOB_ACCOUNT=default
SLURM_JOB_CPUS_PER_NODE=12
SLURM_JOB_GPUS=0
SLURM_JOB_ID=5042618
SLURM_JOB_NAME=5nsx100iter_7days
SLURM_JOB_NODELIST=gpu31
SLURM_JOB_NUM_NODES=1
SLURM_JOB_PARTITION=gpu
SLURM_JOB_QOS=normal
SLURM_JOB_UID=389156
SLURM_JOB_USER=ft18983
SLURM_LOCALID=0
SLURM_MEM_PER_CPU=1000
SLURM_NNODES=1
SLURM_NODEID=0
SLURM_NODELIST=gpu31
SLURM_NODE_ALIASES=(null)
SLURM_NPROCS=12
SLURM_NTASKS=12
SLURM_NTASKS_PER_NODE=12
SLURM_PRIO_PROCESS=0
SLURM_PROCID=0
SLURM_SUBMIT_DIR=/mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE
SLURM_SUBMIT_HOST=bc4login2.bc4.acrc.priv
SLURM_TASKS_PER_NODE=12
SLURM_TASK_PID=25757
SLURM_TOPOLOGY_ADDR=ofacore[01-06].ofaleaf18.gpu31
SLURM_TOPOLOGY_ADDR_PATTERN=switch.switch.node
SSH_CLIENT=137.222.114.247 36626 22
SSH_CONNECTION=137.222.114.247 36626 172.26.2.22 22
SSH_TTY=/dev/pts/22
TERM=xterm
TMPDIR=/tmp
USER=ft18983
WEST_CURRENT_ITER=3
WEST_CURRENT_SEG_DATA_REF=/mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE/traj_segs/000003/000000
WEST_CURRENT_SEG_ID=0
WEST_CURRENT_SEG_INITPOINT_TYPE=SEG_INITPOINT_CONTINUES
WEST_PARENT_DATA_REF=/mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE/traj_segs/000002/000015
WEST_PARENT_ID=15
WEST_PCOORD_RETURN=/tmp/tmpqv0rvms5
WEST_RAND128=32205001152299761018160512778741212529
WEST_RAND16=48985
WEST_RAND32=2027705966
WEST_RAND64=14936058855549925362
WEST_RANDFLOAT=0.261646579791904
WEST_SIM_ROOT=/mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE
WM_PROCESS_INDEX=25
XDG_RUNTIME_DIR=/run/user/389156
XDG_SESSION_ID=34998107
_=/usr/bin/env
_CE_CONDA=
_CE_M=
_LMFILES_=/mnt/storage/easybuild/modules/local/libs/cuda/9.0-gcc-5.4.0-2.26.lua:/mnt/storage/easybuild/modules/local/libs/cudnn/9.0-cuda-9.0.lua:/mnt/storage/easybuild/modules/all/GCCcore/6.3.0.lua:/mnt/storage/easybuild/modules/all/binutils/2.27-GCCcore-6.3.0.lua:/mnt/storage/easybuild/modules/all/GCC/6.3.0-2.27.lua:/mnt/storage/easybuild/modules/all/numactl/2.0.11-GCC-6.3.0-2.27.lua:/mnt/storage/easybuild/modules/all/hwloc/1.11.5-GCC-6.3.0-2.27.lua:/mnt/storage/easybuild/modules/all/OpenMPI/2.0.2-GCC-6.3.0-2.27.lua:/mnt/storage/easybuild/modules/local/apps/amber18/tools19-cuda-mpi-gnu-6.3.0.lua
_ModuleTable001_=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
_ModuleTable002_=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
_ModuleTable003_=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+ cd /mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE
+ mkdir -pv /mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE/traj_segs/000003/000000
mkdir: created directory '/mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE/traj_segs/000003/000000'
+ cd /mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE/traj_segs/000003/000000
+ ln -sv /mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE/common_files/3TI6_IRHY_implicit.prmtop .
'./3TI6_IRHY_implicit.prmtop' -> '/mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE/common_files/3TI6_IRHY_implicit.prmtop'
+ '[' SEG_INITPOINT_CONTINUES = SEG_INITPOINT_CONTINUES ']'
+ sed s/RAND/48985/g /mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE/common_files/md.in
+ ln -sv /mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE/traj_segs/000002/000015/seg.rst ./parent.rst
'./parent.rst' -> '/mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE/traj_segs/000002/000015/seg.rst'
+ /mnt/storage/software/apps/Amber18-MPI/amber18/bin/pmemd.cuda -O -i md.in -p 3TI6_IRHY_implicit.prmtop -c parent.rst -r seg.rst -x seg.nc -o seg.log -inf seg.nfo
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
+ python /mnt/storage/scratch/ft18983/Neuraminidase/WESTPA_1.0/ChemDyME_NA_OSE/common_files/chemdyme_progress_coord.py