GEAR Agora example doesn't work out of box
Code compiled with --with-subgrid=GEAR
on latest master.
Here's the full log:
$ ./run.sh
rm: cannot remove 'agora_disk_0*.hdf5': No such file or directory
changeType.py:84: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
f = File(filename)
Welcome to the cosmological hydrodynamical code
______ _________________
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\__ \| | /| / // // /_ / /
___/ /| |/ |/ // // __/ / /
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SPH With Inter-dependent Fine-grained Tasking
Version : 0.8.5
Revision: v0.8.5-1113-ge0750f24, Branch: master, Date: 2020-08-25 11:24:31 +0200
Webpage : www.swiftsim.com
Config. options: '--with-metis=/home/mivkov/local/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-10.2.0/metis-5.1.0-2iv3olcu3e3ywtvaie7kbtabomkkfzy7 --with-jemalloc=/home/mivkov/local/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-10.2.0/jemalloc-5.2.1-zjrgbronlscjuvupwikgwfj6ksarxcpz --with-hdf5=/home/mivkov/local/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-10.2.0/hdf5-1.10.6-wlomg2xucgt6zxzvwsql2m3wnjziplqm --with-grackle=/home/mivkov/local/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-10.2.0/grackle-3.2-v6mxvhuttcmlzo7datm6hgxuohkqatsu --disable-mpi --disable-doxygen-doc --disable-hand-vec --with-hydro=gadget2 --with-subgrid=GEAR'
Compiler: GCC, Version: 10.2.0
CFLAGS : '-O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -ffast-math -funroll-loops -march=skylake -mavx2 -pthread -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -Wall -Wextra -Wno-unused-parameter -Wshadow -Werror -Wstrict-prototypes'
HDF5 library version: 1.10.6
FFTW library version: 3.x (details not available)
GSL library version: 2.5
[00000.0] main: CPU frequency used for tick conversion: 2111986790 Hz
[00000.0] main: Running on: mivkov-lenovo
[00000.0] main: sizeof(part) is 288 bytes.
[00000.0] main: sizeof(xpart) is 128 bytes.
[00000.0] main: sizeof(sink) is 96 bytes.
[00000.0] main: sizeof(spart) is 320 bytes.
[00000.0] main: sizeof(bpart) is 96 bytes.
[00000.0] main: sizeof(gpart) is 96 bytes.
[00000.0] main: sizeof(multipole) is 192 bytes.
[00000.0] main: sizeof(grav_tensor) is 144 bytes.
[00000.0] main: sizeof(task) is 96 bytes.
[00000.0] main: sizeof(cell) is 1088 bytes.
[00000.0] main: Reading runtime parameters from file 'agora_disk.yml'
[00000.0] main: Internal unit system: U_M = 1.988480e+43 g.
[00000.0] main: Internal unit system: U_L = 3.085678e+21 cm.
[00000.0] main: Internal unit system: U_t = 3.085678e+16 s.
[00000.0] main: Internal unit system: U_I = 1.000000e+00 A.
[00000.0] main: Internal unit system: U_T = 1.000000e+00 K.
[00000.0] phys_const_print: Gravitational constant = 4.301069e+04
[00000.0] phys_const_print: Speed of light = 2.997925e+05
[00000.0] phys_const_print: Planck constant = 1.079902e-96
[00000.0] phys_const_print: Boltzmann constant = 6.943238e-70
[00000.0] phys_const_print: Thomson cross-section = 6.986845e-68
[00000.0] phys_const_print: Electron-Volt = 8.057293e-66
[00000.0] phys_const_print: Proton mass = 8.411560e-68
[00000.0] phys_const_print: Year = 1.022690e-09
[00000.0] phys_const_print: Astronomical Unit = 4.848137e-09
[00000.0] phys_const_print: Parsec = 1.000000e-03
[00000.0] phys_const_print: Solar mass = 9.999648e-11
[00000.0] phys_const_print: H_0 / h = 100 km/s/Mpc = 1.000000e-01
[00000.0] feedback/GEAR/stellar_evolution.c:stellar_evolution_read_elements():399: The chemistry table should contain the metals in the last column (found Metals%�y)
Changing smoothing length to be Gadget compatible
Traceback (most recent call last):
File "cleanupSwift.py", line 12, in <module>
copyfile(filename, out)
File "/home/mivkov/virtualenv/default/lib/python3.6/shutil.py", line 120, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: 'agora_disk_0000.hdf5'
Edited by Mladen Ivkovic