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View Code? Open in Web Editor NEWTools to make using job arrays a lot more convenient.
License: GNU General Public License v3.0
Tools to make using job arrays a lot more convenient.
License: GNU General Public License v3.0
Hi.
Apparently, with atools/1.4.5 the acreate
command is built against a python version which does not recognize the "sys" package (or not imported). The main issue is reported in service desk ticket 31609268.
$ acreate single_RG.pbs > single_RG_puls.pbs Traceback (most recent call last): File "/vsc-hard-mounts/leuven-apps/skylake/2018a/software/atools/1.4.5/bin/../lib/acreate.py", line 73, in <module> sys.stderr.write(msg) NameError: name 'sys' is not defined
Thanks
Ehsan
I need to run autoreconf -f
before I can run the configure script.
Can the 1.4.1 release also be tagged?
I naively tried to run atools
on top of Python 3, but quickly ran into trouble:
$ acreate --help
Traceback (most recent call last):
File "/software/atools/1.4.7-GCCcore-8.3.0-Python-3.7.4/bin/../lib/acreate.py", line 8, in <module>
from vsc.atools.config import get_default_shell, ConfigFileError
File "/software/atools/1.4.7-GCCcore-8.3.0-Python-3.7.4/lib/vsc/atools/config.py", line 3, in <module>
import ConfigParser
ModuleNotFoundError: No module named 'ConfigParser'
Are there any plans to (also) support Python 3?
Hi,
I noticed the following issue when running through the example files, using atools 1.4.7 (Github tar.gz
file) with system Python 2.7.5. I verified this on another (Linux) system with a newly download copy of atools 1.4.7 and system Python 2.7.18.
On the single_column_data.csv file in the examples/
directory, aenv
runs successfully using the --no_sniffer option:
PBS_ARRAYID=1 ./aenv --no_sniffer --data ../examples/single_column_data.csv
and returns the expected result
export file="./abc.txt"
However, when running arange
on the same file, using the same options:
./arange --no_sniffer --data ../examples/single_column_data.csv
I get the following error:
Traceback (most recent call last):
File "<atools_dir>/bin/../lib/arange.py", line 42, in
sniff=options.sniff, no_sniffer=options.no_sniffer
File "<atools_dir>/lib/vsc/atools/work_analysis.py", line 60, in compute_items_todo
todo = _compute_data_ids(data_files, sniff)
File "<atools_dir>/lib/vsc/atools/work_analysis.py", line 40, in _compute_data_ids
dialect = sniffer.sniff(csv_file.read(sniff))
File "/usr/lib64/python2.7/csv.py", line 188, in sniff
raise Error, "Could not determine delimiter"
_csv.Error: Could not determine delimiter
arange
sometimes does work on single column files, albeit for the wrong reason. For single column files, arange
seems to return the correct result only if the first letter of the first data line is equal to the first letter of the column heading. For example, running arange --no_sniffer --data <file>
on a file with following content
f
a
returns the above error, where running it on a file with following content
f
f
successfully returns 1. Hence, this is likely related to the way the delimiter is detected by arange
, especially because aenv
works as expected in both cases.
Adding no_sniffer
as a third argument in the call to _compute_data_ids
on line 60 of lib/vsc/atools/work_analysis.py
fixed it for me. As I'm currently unaware of possible consequences in the rest of the code, I have not yet submitted this as a pull request.
Hello Geert Jan
I'm using the GitHub version and a system Python 2.7.5.
Following command is executed without problems
./acreate ../examples/standard.pbs --data ../examples/data.csv
but
./acreate --data ../examples/data.csv ../examples/standard.pbs
returns
acreate.py: error: too few arguments
Since the problem seems to be related to nargs='*'
for --data
I would suggest to update the documentation and write the above as
./acreate --data ../examples/data.csv -- ../examples/standard.pbs
Regards
Stefan
Is there a way to build atools on RHEL 7.x? The documented procedure fails due to the configure script wanting a newer version of aclocal than ships with RHEL 7.6.
troy@owens-login01:~/src$ git clone https://github.com/gjbex/atools.git atools-git
Cloning into 'atools-git'...
remote: Enumerating objects: 142, done.
remote: Counting objects: 100% (142/142), done.
remote: Compressing objects: 100% (85/85), done.
remote: Total 1179 (delta 77), reused 97 (delta 50), pack-reused 1037
Receiving objects: 100% (1179/1179), 900.42 KiB | 0 bytes/s, done.
Resolving deltas: 100% (673/673), done.
troy@owens-login01:~/src$ cd atools-git/
troy@owens-login01:~/src/atools-git$ ./configure --prefix=$HOME/src/atools-inst --with-batchsystem=torque
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking how to create a pax tar archive... gnutar
configure: Setting Python to /usr/bin/python...
configure: Creatign atools.conf...
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bin/Makefile
config.status: creating conf/Makefile
config.status: creating lib/Makefile
config.status: creating lib/vsc/Makefile
config.status: creating lib/vsc/atools/Makefile
config.status: creating reduce/Makefile
config.status: creating tmpls/Makefile
troy@owens-login01:~/src/atools-git$ make install
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /users/sysp/troy/src/atools-git/missing aclocal-1.16
/users/sysp/troy/src/atools-git/missing: line 81: aclocal-1.16: command not found
WARNING: 'aclocal-1.16' is missing on your system.
You should only need it if you modified 'acinclude.m4' or
'configure.ac' or m4 files included by 'configure.ac'.
The 'aclocal' program is part of the GNU Automake package:
<http://www.gnu.org/software/automake>
It also requires GNU Autoconf, GNU m4 and Perl in order to run:
<http://www.gnu.org/software/autoconf>
<http://www.gnu.org/software/m4/>
<http://www.perl.org/>
make: *** [aclocal.m4] Error 127
troy@owens-login01:~/src/atools-git$ grep aclocal configure
ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
troy@owens-login01:~/src/atools-git$ grep am__api_version configure
am__api_version='1.16'
ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
troy@owens-login01:~/src/atools-git$ which aclocal
/usr/bin/aclocal
troy@owens-login01:~/src/atools-git$ aclocal --version
aclocal (GNU automake) 1.13.4
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv2+: GNU GPL version 2 or later <http://gnu.org/licenses/gpl-2.0.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Tom Tromey <[email protected]>
and Alexandre Duret-Lutz <[email protected]>.
troy@owens-login01:~/src/atools-git$ cat /etc/redhat-release
Red Hat Enterprise Linux Server release 7.6 (Maipo)
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