make[2]: Entering directory `/apps/amber18/test' cd cuda && make -k test.pmemd.cuda.MPI PREC_MODEL=DPFP make[3]: Entering directory `/apps/amber18/test/cuda' --------------------------------------------- Running Extended CUDA Implicit solvent tests. Precision Model = DPFP --------------------------------------------- cd trpcage/ && ./Run_md_trpcage DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run_md_trpcage: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd myoglobin/ && ./Run_md_myoglobin DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run_md_myoglobin: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd myoglobin/ && ./Run_md_myoglobin_igb7 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run_md_myoglobin_igb7: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd myoglobin/ && ./Run_md_myoglobin_igb8 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run_md_myoglobin_igb8: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd myoglobin/ && ./Run_md_myoglobin_igb8_gbsa DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run_md_myoglobin_igb8_gbsa: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd cnstph/implicit/ && ./Run.cnstph DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.cnstph: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd cnste/implicit/ && ./Run.cnste DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.cnste: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd cnstphe/implicit/ && ./Run.cnstphe DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.cnstphe: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd chamber/dhfr/ && ./Run.dhfr_charmm.md DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr_charmm.md: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd chamber/dhfr_cmap/ && ./Run.dhfr_charmm.md DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr_charmm.md: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nucleosome/ && ./Run_md.1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run_md.1: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nucleosome/ && ./Run_md.2 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run_md.2: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd gamd/rna_gb && ./Run.gb.gamd1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.gb.gamd1: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd gamd/rna_gb && ./Run.gb.gamd2 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.gb.gamd2: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd gamd/rna_gb && ./Run.gb.gamd3 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.gb.gamd3: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd amd/rna_gb && ./Run.gb.amd1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.gb.amd1: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd amd/rna_gb && ./Run.gb.amd2 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.gb.amd2: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd amd/rna_gb && ./Run.gb.amd3 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.gb.amd3: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nmropt/gb/angle/ && ./Run.nmropt_1angle_gb DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.nmropt_1angle_gb: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nmropt/gb/distance/ && ./Run.dist_gb DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- errori: label not found. make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nmropt/gb/distance_COM/ && ./Run.distCOM_gb DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.distCOM_gb: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nmropt/gb/distance_COM/ && ./Run.distr6av_gb DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.distr6av_gb: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nmropt/gb/jar_distance_COM/ && ./Run.jar_gb DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.jar_gb: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nmropt/gb/jar_distance/ && ./Run.jar_gb DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.jar_gb: Program Error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nmropt/gb/jar_torsion/ && ./Run.jar_torsion DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.jar_torsion: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nmropt/gb/nmropt_1_torsion/ && ./Run.nmropt_1_torsion DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.nmropt_1_torsion: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nmropt/gb/tautp/ && ./Run.nmropt_1tautp_gb DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.nmropt_1tautp_gb: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) cd nmropt/gb/temp/ && ./Run.nmropt_1temp_gb DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.nmropt_1temp_gb: Program error make[3]: [test.pmemd.cuda.gb] Error 1 (ignored) --------------------------------------------- Running Extended CUDA Explicit solvent tests. Precision Model = DPFP --------------------------------------------- cd FactorIX_NVE/ && ./Run.FactorIX_NVE DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.FactorIX_NVE: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd 4096wat/ && ./Run.pure_wat DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pure_wat: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd 4096wat/ && ./Run.pure_wat_fswitch DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pure_wat_fswitch: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd 4096wat/ && ./Run.pure_wat_efield DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pure_wat_efield: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd 4096wat_oct/ && ./Run.pure_wat_oct_NVE DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pure_wat_oct_NVE: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd 4096wat_oct/ && ./Run.pure_wat_oct_NVT_NTT1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pure_wat_oct_NVT_NTT1: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd 4096wat_oct/ && ./Run.pure_wat_oct_NPT_NTT1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pure_wat_oct_NPT_NTT1: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd large_solute_count/ && ./Run.ntb2_ntt1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.ntb2_ntt1: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd jac/ && ./Run.jac DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.jac: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd dhfr/ && ./Run.dhfr DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd dhfr/ && ./Run.dhfr.ntr1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr.ntr1: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd dhfr/ && ./Run.dhfr.ntb2 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr.ntb2: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd dhfr/ && ./Run.dhfr.ntb2_ntt1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr.ntb2_ntt1: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd dhfr/ && ./Run.dhfr.ntb2_ntt1_ntr1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr.ntb2_ntt1_ntr1: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd dhfr/ && ./Run.dhfr.noshake DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr.noshake: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd chamber/dhfr_pbc/ && ./Run.dhfr_pbc_charmm_noshake.md DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr_pbc_charmm_noshake.md: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd chamber/dhfr_cmap_pbc/ && ./Run.dhfr_cmap_pbc_charmm.md DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr_cmap_pbc_charmm.md: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd chamber/dhfr_cmap_pbc/ && ./Run.dhfr_cmap_pbc_charmm_NPT.md DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr_cmap_pbc_charmm_NPT.md: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd chamber/dhfr_cmap_pbc/ && ./Run.dhfr_cmap_pbc_charmm_noshake.md DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dhfr_cmap_pbc_charmm_noshake.md: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd ips/ && ./Run.ips DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.ips: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd gamd/dhfr_pme && ./Run.pme.gamd1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pme.gamd1: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd gamd/dhfr_pme && ./Run.pme.gamd2 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pme.gamd2: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd gamd/dhfr_pme && ./Run.pme.gamd3 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pme.gamd3: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd amd/dhfr_pme && ./Run.pme.amd1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pme.amd1: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd amd/dhfr_pme && ./Run.pme.amd2 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pme.amd2: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd amd/dhfr_pme && ./Run.pme.amd3 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.pme.amd3: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd amd/gact_ips && ./Run.ips.amd1 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.ips.amd1: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd amd/gact_ips && ./Run.ips.amd2 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.ips.amd2: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd amd/gact_ips && ./Run.ips.amd3 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.ips.amd3: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd scaledMD && ./Run.scaledMD DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.scaledMD: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd nmropt/pme/angle/ && ./Run.nmropt_1angle_pbc DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.nmropt_1angle_pbc: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd nmropt/pme/distance/ && ./Run.dist_pbc DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.dist_pbc: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd nmropt/pme/distance_COM/ && ./Run.distCOM_pbc DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.distCOM_pbc: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd nmropt/pme/distance_COM/ && ./Run.multi-distCOM-multi-dist_pbc DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.multi-distCOM-multi-dist_pbc: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd nmropt/pme/distance_COM/ && ./Run.multi-distr6av_pbc DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.multi-distr6av_pbc: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd nmropt/pme/jar_distance_COM/ && ./Run.jar_pbc DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.jar_pbc: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd nmropt/pme/jar_distance/ && ./Run.jar_pbc DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.jar_pbc: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd nmropt/pme/jar_torsion/ && ./Run.jar_torsion DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.jar_torsion: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd nmropt/pme/nmropt_1_torsion/ && ./Run.nmropt_1_torsion DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.nmropt_1_torsion: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd nmropt/pme/tautp/ && ./Run.nmropt_1tautp_pbc DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.nmropt_1tautp_pbc: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd nmropt/pme/temp/ && ./Run.nmropt_1temp_pbc DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.nmropt_1temp_pbc: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd tip4pew/ && ./Run.tip4pew_box_nvt DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.tip4pew_box_nvt: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd tip4pew/ && ./Run.tip4pew_box_npt DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.tip4pew_box_npt: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd tip4pew/ && ./Run.tip4pew_oct_nvt DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.tip4pew_oct_nvt: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd tip4pew/ && ./Run.tip4pew_oct_npt DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.tip4pew_oct_npt: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd tip4pew/ && ./Run.tip4pew_box_npt_mcbar DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.tip4pew_box_npt_mcbar: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd tip4pew/ && ./Run.tip4pew_oct_npt_mcbar DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.tip4pew_oct_npt_mcbar: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd tip5p/ && ./Run.tip5p_box_nvt DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.tip5p_box_nvt: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd tip5p/ && ./Run.tip5p_box_npt DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.tip5p_box_npt: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd tip5p/ && ./Run.tip5p_oct_nvt DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.tip5p_oct_nvt: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd tip5p/ && ./Run.tip5p_oct_npt DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.tip5p_oct_npt: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd HMR/ && ./Run.HMR DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.HMR: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd lipid_npt_tests/ && ./Run_npt_isotropic.lipid14 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run_npt_isotropic.lipid14: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd lipid_npt_tests/ && ./Run_npt_anisotropic.lipid14 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run_npt_anisotropic.lipid14: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd lipid_npt_tests/ && ./Run_npt_semiisotropic.lipid14 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run_npt_semiisotropic.lipid14: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd ff19SB/ && ./Run DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run: Program error make[3]: [test.pmemd.cuda.pme] Error 1 (ignored) cd cellulose/ && ./Run.cellulose_nvt_256_128_128 DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.cellulose_nvt_256_128_128: Program error make[3]: [test.pmemd.cuda.pme.big] Error 1 (ignored) cd cellulose/ && ./Run.cellulose_nvt DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.cellulose_nvt: Program error make[3]: [test.pmemd.cuda.pme.big] Error 1 (ignored) cd cellulose/ && ./Run.cellulose_npt DPFP /apps/amber18/include/netcdf.mod -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./Run.cellulose_npt: Program error make[3]: [test.pmemd.cuda.pme.big] Error 1 (ignored) cd remd && make test make[4]: Entering directory `/apps/amber18/test/cuda/remd' ./test_cuda_remd.sh -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- ./test_cuda_remd.sh: line 24: [: -eq: unary operator expected ./test_cuda_remd.sh: line 26: [: -eq: unary operator expected CUDA REMD tests can only be run with 2 or 4 threads ( currently). make[4]: Leaving directory `/apps/amber18/test/cuda/remd' cd nfe/ && ./run-pmemd-parallel.sh DPFP /apps/amber18/include/netcdf.mod >>>>>>> doing 'abmd_ANALYSIS' possible FAILURE: file mdout does not exist. ============================================================== possible FAILURE: file monitor.txt does not exist. ============================================================== >>>>>>> doing 'abmd_FLOODING' possible FAILURE: file mdout does not exist. ============================================================== possible FAILURE: file monitor.txt does not exist. ============================================================== /apps/amber18/bin/ncdump: umbrella.nc: No such file or directory ncgen: - line 1: syntax error, unexpected $end, expecting NETCDF /apps/amber18/bin/ncdump: ncdump.tmp: No such file or directory diffing save.pmemd/umbrella.save.ncdump with umbrella.ncdump file ddtmp.umbrella.ncdump is short possible FAILURE: check umbrella.ncdump.dif ============================================================== /apps/amber18/bin/ncdump: wt_umbrella.nc: No such file or directory ncgen: - line 1: syntax error, unexpected $end, expecting NETCDF /apps/amber18/bin/ncdump: ncdump.tmp: No such file or directory diffing save.pmemd/wt_umbrella.save.ncdump with wt_umbrella.ncdump file ddtmp.wt_umbrella.ncdump is short possible FAILURE: check wt_umbrella.ncdump.dif ============================================================== >>>>>>> doing 'abmd_UMBRELLA' possible FAILURE: file mdout does not exist. ============================================================== possible FAILURE: file monitor.txt does not exist. ============================================================== >>>>>>> doing 'smd' possible FAILURE: file mdout does not exist. ============================================================== possible FAILURE: file smd.txt does not exist. ============================================================== >>>>>>> doing 'smd2' -------------------------------------------------------------------------- mpirun has detected an attempt to run as root. Running as root is *strongly* discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state. We strongly suggest that you run mpirun as a non-root user. You can override this protection by adding the --allow-run-as-root option to the cmd line or by setting two environment variables in the following way: the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and add one more layer of certainty that you want to do so. We reiterate our advice against doing so - please proceed at your own risk. -------------------------------------------------------------------------- possible FAILURE: file mdout does not exist. ============================================================== possible FAILURE: file work.txt does not exist. ============================================================== >>>>>>> doing 'bbmd' This test case (/apps/amber18/test/cuda/nfe/bbmd) requires a least 4 mpi threads. The number of mpi threads must also be a multiple of 4 and not more than 256. Not running test, exiting ..... >>>>>>> doing 'mwabmd' This test case (/apps/amber18/test/cuda/nfe/mwabmd) requires a least 4 mpi threads. The number of mpi threads must also be a multiple of 4 and not more than 256. Not running test, exiting ..... >>>>>>> doing 'premd' This test case (/apps/amber18/test/cuda/nfe/premd) requires a least 4 mpi threads. The number of mpi threads must also be a multiple of 4 and not more than 256. Not running test, exiting ..... >>>>>>> doing 'abremd' This test case (/apps/amber18/test/cuda/nfe/abremd) requires a least 4 mpi threads. The number of mpi threads must also be a multiple of 4 and not more than 256. Not running test, exiting ..... cd neb-testcases/neb_gb_partial && ./Run.neb_gb_partial DPFP /apps/amber18/include/netcdf.mod This test case requires 4 mpi threads. Not running test, exiting..... cd neb-testcases/neb_gb_full && ./Run.neb_gb_full DPFP /apps/amber18/include/netcdf.mod This test case requires 4 mpi threads. Not running test, exiting..... cd neb-testcases/neb_explicit && ./Run.neb_explicit DPFP /apps/amber18/include/netcdf.mod This test case requires 4 mpi threads. Not running test, exiting..... make[3]: Leaving directory `/apps/amber18/test/cuda' make[2]: Leaving directory `/apps/amber18/test' 0 file comparisons passed 12 file comparisons failed (0 ignored) 176 tests experienced errors