Parse error for abinit build options
antoine-levitt opened this issue · comments
I get a parse error in abipy:
In [3]: abipy.abilab.abicheck()
AbiPy Manager:
[Qadapter 0]
ShellAdapter:localhost
Hardware:
num_nodes: 1, sockets_per_node: 1, cores_per_socket: 2, mem_per_node 4096,
Qadapter selected: 0
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-3-a999053d8689> in <module>()
----> 1 abipy.abilab.abicheck()
/usr/local/lib/python3.6/dist-packages/abipy/abilab.py in abicheck(verbose)
334 if manager is not None:
335 cprint("AbiPy Manager:\n%s\n" % str(manager), color="green")
--> 336 build = AbinitBuild(manager=manager)
337 if not build.has_netcdf: app("Abinit executable does not support netcdf")
338 cprint("Abinitbuild:\n%s" % str(build), color="magenta")
/usr/local/lib/python3.6/dist-packages/abipy/flowtk/tasks.py in __init__(self, workdir, manager)
1163 self.has_netcdf = "netcdf" in line
1164 if "openMP support" in line: self.has_omp = yesno2bool(line)
-> 1165 if "Parallel build" in line: self.has_mpi = yesno2bool(line)
1166 if "Parallel I/O" in line: self.has_mpiio = yesno2bool(line)
1167
/usr/local/lib/python3.6/dist-packages/abipy/flowtk/tasks.py in yesno2bool(line)
1155 def yesno2bool(line):
1156 ans = line.split()[-1].lower()
-> 1157 return dict(yes=True, no=False, auto=True)[ans]
1158
1159 # Parse info.
KeyError: ':'
I think this is because
antoine@beta ~/abipy $ abinit -b
DATA TYPE INFORMATION:
REAL: Data type name: REAL(DP)
Kind value: 8
Precision: 15
Smallest nonnegligible quantity relative to 1: 0.22204460E-015
Smallest positive number: 0.22250739E-307
Largest representable number: 0.17976931E+309
INTEGER: Data type name: INTEGER(default)
Kind value: 4
Bit size: 32
Largest representable number: 2147483647
LOGICAL: Data type name: LOGICAL
Kind value: 4
CHARACTER: Data type name: CHARACTER Kind value: 1
MPI-IO support is OFF
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
CPP options activated during the build:
CC_GNU CXX_GNU FC_GNU
HAVE_FC_ALLOCATABLE_DT... HAVE_FC_ASYNC HAVE_FC_BACKTRACE
HAVE_FC_COMMAND_ARGUMENT HAVE_FC_COMMAND_LINE HAVE_FC_CONTIGUOUS
HAVE_FC_CPUTIME HAVE_FC_EXIT HAVE_FC_FLUSH
HAVE_FC_GAMMA HAVE_FC_GETENV HAVE_FC_IEEE_ARITHMETIC
HAVE_FC_IEEE_EXCEPTIONS HAVE_FC_INT_QUAD HAVE_FC_IOMSG
HAVE_FC_ISO_C_BINDING HAVE_FC_ISO_FORTRAN_2008 HAVE_FC_LONG_LINES
HAVE_FC_MOVE_ALLOC HAVE_FC_ON_THE_FLY_SHAPE HAVE_FC_PRIVATE
HAVE_FC_PROTECTED HAVE_FC_SHIFTLR HAVE_FC_STREAM_IO
HAVE_FC_SYSTEM HAVE_FFTW3 HAVE_FFTW3_THREADS
HAVE_FORTRAN2003 HAVE_HDF5 HAVE_LIBPAW_ABINIT
HAVE_LIBTETRA_ABINIT HAVE_LIBXC HAVE_LINALG_AXPBY
HAVE_LINALG_GEMM3M HAVE_NETCDF HAVE_NETCDF_FORTRAN
HAVE_NUMPY HAVE_OS_LINUX HAVE_TIMER_ABINIT
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
=== Build Information ===
Version : 9.0.3
Build target : x86_64_linux_gnu7.5
Build date : 20200429
=== Compiler Suite ===
C compiler : gnu7.5
C++ compiler : gnu7.5
Fortran compiler : gnu7.5
CFLAGS : -g -O2 -mtune=native -march=native
CXXFLAGS : -g -O2 -mtune=native -march=native
FCFLAGS : -g -ffree-line-length-none -I/usr//include -I/usr//include
FC_LDFLAGS :
=== Optimizations ===
Debug level : @abi_debug_flavor@
Optimization level : @abi_optim_flavor@
Architecture : unknown_unknown
=== Multicore ===
Parallel build :
Parallel I/O :
openMP support :
GPU support :
=== Connectors / Fallbacks ===
LINALG flavor : netlib+openblas
FFT flavor : fftw3-threads
HDF5 : yes
NetCDF : yes
NetCDF Fortran : yes
LibXC : yes
Wannier90 : no
=== Experimental features ===
Exports :
GW double-precision :
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
-O2 -mtune=native -march=native
Optimizations for 43_ptgroups:
-O0
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
and it's failing to parse the "multicore" section.
This is for abinit 9.0.3.
Hi Antoine,
Yes, Abinit9 has changed the format used to print the build option.
I've pushed a temporary fix in d55d8ec
(see modifications in flowtk.tasks.py)
You may want to patch your version of tasks.py with the one found in the develop branch
I haven't yet released a new version of AbiPy on pypi because Abinit9 is a beta-release and I was not expecting users to run AbiPy calculations with Abinit9.
The AbiPy post-processing tools should work both with Abinit8 and Abinit9 because we haven't changed the netcdf format but at the level of the workflows there are some new features implemented in Abinit that we plan to support in AbiPy.
All these changes will be gradually integrated when a stable Abinit9 is released.
Hi! Thanks for this, so it's my bad for going with abinit9 - I just picked the first link on the abinit website actually... I'll try with abinit8
OK for some reason I can't get abinit8 to build, so I've tried monkey patching tasks.py (adding those two lines in your commit) and now abipy complains my abinit executable doesn't have netcdf, even though abinit -b answers
=== Connectors / Fallbacks ===
LINALG flavor : netlib+openblas
FFT flavor : fftw3-threads
HDF5 : yes
NetCDF : yes
NetCDF Fortran : yes
LibXC : yes
Wannier90 : no
Can you try the latest version of tasks.py available here ?
There should be a check for the presence of "Netcdf Fortran" that should work with Abinit9:
# Parse info.
# flavor options were used in Abinit v8
for line in self.info.splitlines():
if "Version" in line: self.version = line.split()[-1]
if "TRIO flavor" in line:
self.has_netcdf = "netcdf" in line
if "NetCDF Fortran" in line:
self.has_netcdf = yesno2bool(line)yay, it works! thanks!