loading system configuration loading override configuration from /zhome/89/0/38697/mxtest/mctest/../mccodelib/mcxtrace-test/McXtrace-1.x_CPU_MPICC/mccode_config.json INFO: Using directory: "2" INFO: Using existing c-file: ./Test_SAXS.c INFO: Using existing binary: ./Test_SAXS.out INFO: === INFO: Using system default number of mpirun -np processes -------------------------------------------------------------------------- By default, for Open MPI 4.0 and later, infiniband ports on a device are not used by default. The intent is to use UCX for these devices. You can override this policy by setting the btl_openib_allow_ib MCA parameter to true. Local host: n-62-29-31 Local adapter: mlx4_0 Local port: 1 -------------------------------------------------------------------------- -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: n-62-29-31 Local device: mlx4_0 -------------------------------------------------------------------------- Simulation 'Test_SAXS' (/zhome/89/0/38697/xTESTS/2022-12-01/McXtrace-1.x_CPU_MPICC_1e7/Test_SAXS/Test_SAXS.instr): running on 10 nodes (master is 'n-62-29-31', MPI version 3.1). [Test_SAXS] Initialize Initializing protein structure... 3v03.pdb PDB file located... [Test_SAXS] Initialize Initializing protein structure... 3v03.pdb PDB file located... [Test_SAXS] Initialize Initializing protein structure... 3v03.pdb PDB file located... Calculating scattering from 1160 residues... Creating protein structure... [Test_SAXS] Initialize Initializing protein structure... Calculating scattering from 1160 residues... Creating protein structure... [Test_SAXS] Initialize Initializing protein structure... 3v03.pdb PDB file located... Calculating scattering from 1160 residues... 3v03.pdb PDB file located... Creating protein structure... Initializations complete... Calculating scattering from 1160 residues... Creating protein structure... [Test_SAXS] Initialize Initializing protein structure... Calculating scattering from 1160 residues... Creating protein structure... 3v03.pdb PDB file located... [Test_SAXS] Initialize Initializing protein structure... 3v03.pdb PDB file located... [Test_SAXS] Initialize Initializing protein structure... 3v03.pdb PDB file located... Initializations complete... Initializations complete... Calculating scattering from 1160 residues... Creating protein structure... Calculating scattering from 1160 residues... Creating protein structure... Initializations complete... Calculating scattering from 1160 residues... Creating protein structure... Initializations complete... [Test_SAXS] Initialize Initializing protein structure... 3v03.pdb PDB file located... Initializations complete... Initializations complete... Initializations complete... Calculating scattering from 1160 residues... Creating protein structure... [Test_SAXS] Initialize Initializing protein structure... 3v03.pdb PDB file located... Calculating scattering from 1160 residues... Creating protein structure... Initializations complete... Initializations complete... Initializing protein structure... 6lyz.pdb PDB file located... Initializing protein structure... 6lyz.pdb PDB file located... Calculating scattering from 129 residues... Initializing arrays... Creating protein structure... Calculating scattering from 129 residues... Initializing arrays... Creating protein structure... Initializing protein structure... Computing scattering from protein... 6lyz.pdb PDB file located... Computing scattering from protein... Calculating scattering from 129 residues... Initializing arrays... Creating protein structure... Computing scattering from protein... Initializing protein structure... 6lyz.pdb PDB file located... Calculating scattering from 129 residues... Initializing arrays... Creating protein structure... Computing scattering from protein... Initializing protein structure... Initializing protein structure... 6lyz.pdb PDB file located... Calculating scattering from 129 residues... Initializing arrays... Creating protein structure... 6lyz.pdb PDB file located... Computing scattering from protein... Calculating scattering from 129 residues... Initializing arrays... Creating protein structure... Computing scattering from protein... Initializing protein structure... 6lyz.pdb PDB file located... Calculating scattering from 129 residues... Initializing arrays... Creating protein structure... Initializing protein structure... 6lyz.pdb PDB file located... Computing scattering from protein... Calculating scattering from 129 residues... Initializing arrays... Creating protein structure... Computing scattering from protein... Initializing protein structure... 6lyz.pdb PDB file located... Calculating scattering from 129 residues... Initializing arrays... Creating protein structure... Computing scattering from protein... Initializing protein structure... 6lyz.pdb PDB file located... Calculating scattering from 129 residues... Initializing arrays... Creating protein structure... Computing scattering from protein... [n-62-29-31:08148] 9 more processes have sent help message help-mpi-btl-openib.txt / ib port not selected [n-62-29-31:08148] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages [n-62-29-31:08148] 9 more processes have sent help message help-mpi-btl-openib.txt / error in device init Initializations complete... Initializations complete... Initializations complete... Initializations complete... Initializations complete... Initializations complete... Initializations complete... Initializations complete... Initializations complete... Initializations complete... Finally [Test_SAXS: 2]. Time: 1 [s] Finally [Test_SAXS: 2]. Time: 1 [s] Finally [Test_SAXS: 2]. Time: 1 [s] Finally [Test_SAXS: 2]. Time: 1 [s] Finally [Test_SAXS: 2]. Time: 1 [s] Finally [Test_SAXS: 2]. Time: 1 [s] Finally [Test_SAXS: 2]. Time: 1 [s] Save [Test_SAXS] Finally [Test_SAXS: 2]. Time: 1 [s] Finally [Test_SAXS: 2]. Time: 1 [s] Detector: Monitor_I=2.79308e-14 Monitor_ERR=2.02225e-16 Monitor_N=2.94395e+06 "PSDMonitor.dat" Detector: QMonitor_I=1.56374e-09 QMonitor_ERR=1.85432e-11 QMonitor_N=4.55561e+06 "RDetector.dat" Detector: QMonitor_I=6.35504e-09 QMonitor_ERR=7.53757e-11 QMonitor_N=4.55561e+06 "QDetector.dat" Finally [Test_SAXS: 2]. Time: 2 [s] INFO: Placing instr file copy /zhome/89/0/38697/xTESTS/2022-12-01/McXtrace-1.x_CPU_MPICC_1e7/Test_SAXS/Test_SAXS.instr in dataset 2