Running Spinetoolbox from command line.

[IngridJSJ]

Hello,
I have now access to a HPC and would like to know if I can run my project there.
So, is it possible to run spinetoolbox worfklow as a script?

Also I tried to install spinetoolbox in linux but it didnt run as smoothly.
when trying to run
python -m pipx install git+https://github.com/Spine-project/spinetoolbox-dev
I got these errors

Building wheel for pyodbc (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/isanchezjimene/.conda/envs/spinetoolbox-dev/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-l536ksqz/pyodbc_83bd7cf51b4e4bc197a59d7c90436bd9/setup.py'"'"'; file='"'"'/tmp/pip-install-l536ksqz/pyodbc_83bd7cf51b4e4bc197a59d7c90436bd9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-4u7x4v36
cwd: /tmp/pip-install-l536ksqz/pyodbc_83bd7cf51b4e4bc197a59d7c90436bd9/
Complete output (14 lines):
running bdist_wheel
running build
running build_ext
creating build
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/src
/apps/arch/2022r2/software/linux-rhel8-skylake_avx512/gcc-8.5.0/gcc-11.2.0-midhpa4emjkjgec276wnpdtxr7f4i5rb/bin/gcc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPYODBC_VERSION=4.0.32 -I/home/isanchezjimene/.conda/envs/spinetoolbox-dev/include/python3.8 -c src/buffer.cpp -o build/temp.linux-x86_64-3.8/src/buffer.o -Wno-write-strings -DHAVE_UNISTD_H -DHAVE_PWD_H -DHAVE_SYS_TYPES_H -DHAVE_LONG_LONG -DSIZEOF_LONG_INT=8 -I/usr/include
cc1plus: warning: command-line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
In file included from src/buffer.cpp:12:
src/pyodbc.h:56:10: fatal error: sql.h: No such file or directory
56 | #include <sql.h>
| ^~~~~~~
compilation terminated.
error: command '/apps/arch/2022r2/software/linux-rhel8-skylake_avx512/gcc-8.5.0/gcc-11.2.0-midhpa4emjkjgec276wnpdtxr7f4i5rb/bin/gcc' failed with exit code 1

ERROR: Failed building wheel for pyodbc
Running setup.py clean for pyodbc
Failed to build pyodbc
Installing collected packages: spinedb-api, spine-engine, pyodbc, spinetoolbox, spine-items
Attempting uninstall: spinedb-api
Found existing installation: spinedb-api 0.22.0.dev0
Uninstalling spinedb-api-0.22.0.dev0:
Successfully uninstalled spinedb-api-0.22.0.dev0
Running setup.py develop for spinedb-api
Attempting uninstall: spine-engine
Found existing installation: spine-engine 0.17.0.dev0
Uninstalling spine-engine-0.17.0.dev0:
Successfully uninstalled spine-engine-0.17.0.dev0
Running setup.py develop for spine-engine
Running setup.py install for pyodbc ... error
ERROR: Command errored out with exit status 1:
command: /home/isanchezjimene/.conda/envs/spinetoolbox-dev/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-l536ksqz/pyodbc_83bd7cf51b4e4bc197a59d7c90436bd9/setup.py'"'"'; file='"'"'/tmp/pip-install-l536ksqz/pyodbc_83bd7cf51b4e4bc197a59d7c90436bd9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-8053f6n0/install-record.txt --single-version-externally-managed --compile --install-headers /home/isanchezjimene/.conda/envs/spinetoolbox-dev/include/python3.8/pyodbc
cwd: /tmp/pip-install-l536ksqz/pyodbc_83bd7cf51b4e4bc197a59d7c90436bd9/
Complete output (14 lines):
running install
running build
running build_ext
creating build
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/src
/apps/arch/2022r2/software/linux-rhel8-skylake_avx512/gcc-8.5.0/gcc-11.2.0-midhpa4emjkjgec276wnpdtxr7f4i5rb/bin/gcc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPYODBC_VERSION=4.0.32 -I/home/isanchezjimene/.conda/envs/spinetoolbox-dev/include/python3.8 -c src/buffer.cpp -o build/temp.linux-x86_64-3.8/src/buffer.o -Wno-write-strings -DHAVE_UNISTD_H -DHAVE_PWD_H -DHAVE_SYS_TYPES_H -DHAVE_LONG_LONG -DSIZEOF_LONG_INT=8 -I/usr/include
cc1plus: warning: command-line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
In file included from src/buffer.cpp:12:
src/pyodbc.h:56:10: fatal error: sql.h: No such file or directory
56 | #include <sql.h>
| ^~~~~~~
compilation terminated.
error: command '/apps/arch/2022r2/software/linux-rhel8-skylake_avx512/gcc-8.5.0/gcc-11.2.0-midhpa4emjkjgec276wnpdtxr7f4i5rb/bin/gcc' failed with exit code 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/isanchezjimene/.conda/envs/spinetoolbox-dev/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-l536ksqz/pyodbc_83bd7cf51b4e4bc197a59d7c90436bd9/setup.py'"'"'; file='"'"'/tmp/pip-install-l536ksqz/pyodbc_83bd7cf51b4e4bc197a59d7c90436bd9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-8053f6n0/install-record.txt --single-version-externally-managed --compile --install-headers /home/isanchezjimene/.conda/envs/spinetoolbox-dev/include/python3.8/pyodbc Check the logs for full command output.

So is there a way to run smoothly spinetoolbox in linux?

[soininen]

Hi Ingrid,

If you've installed Toolbox on the remote server, and the project directory is available there too, you can execute the project from the command line in "headless" mode without opening the GUI:

python -mspinetoolbox --execute-only /path/to/project-dir/

For more information on the command line options such as how to select specific project items for execution, run

python -mspinetoolbox --help

[soininen]

The installation problem is not really a Toolbox issue but it looks like your system is missing some packages. You could try searching the web for src/pyodbc.h:56:10: fatal error: sql.h: No such file or directory or maybe this discussion provides some help.

[ptsavol]

There's this in the Troubleshooting section of Spine Toolbox's readme.md.

Installation fails on Linux

If Python runs into errors while installing on Linux systems, running the following commands in a terminal may help:

$ sudo apt install libpq-dev
$ sudo apt-get install unixodbc-dev

[IngridJSJ]

Thank you for the answers.
I tried the sudo apt-get install unixodbc-dev but unfortunately this command is not allowed in the HPC...
I will try other things and let you know