From c722cc8ca70d5c51ee5b8a8e7dc098f55dcb1075 Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Mon, 27 Jan 2020 17:31:45 +0000
Subject: [PATCH] tried to run this from surrey pc, got the following error:
/usr/bin/ld: /tmp/ccca3KKm.o: relocation R_X86_64_32 against .rodata.str1.1
can not be used when making a shared object; recompile with -fPIC
/tmp/ccca3KKm.o: error adding symbols: Bad value collect2: error: ld returned
1 exit status
---
requirements.txt | 79 +++++++++++--------
...ltiprocessing_via_population_comparison.py | 6 +-
tests/population/surreypc_errorlog.txt | 42 ++++++++++
tests/python_API_test.py | 2 +-
4 files changed, 90 insertions(+), 39 deletions(-)
create mode 100644 tests/population/surreypc_errorlog.txt
diff --git a/requirements.txt b/requirements.txt
index 4e216d9a3..752b27517 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,49 +1,58 @@
-alabaster==0.7.12
-Babel==2.7.0
+astropy==3.2.1
+attrs==19.1.0
backcall==0.1.0
-binarycpython==0.1
-certifi==2019.9.11
-chardet==3.0.4
-clang==6.0.0.2
+bleach==3.1.0
cycler==0.10.0
-decorator==4.4.1
-docutils==0.15.2
+decorator==4.4.0
+defusedxml==0.6.0
+dill==0.3.1.1
+entrypoints==0.3
h5py==2.10.0
-hawkmoth==0.4
-idna==2.8
-imagesize==1.1.0
-ipython==7.9.0
+ipykernel==5.1.2
+ipython==7.7.0
ipython-genutils==0.2.0
+ipywidgets==7.5.1
+ivs-sse==0.0
jedi==0.15.1
-Jinja2==2.10.3
+Jinja2==2.10.1
+jsonschema==3.0.2
+jupyter==1.0.0
+jupyter-client==5.3.1
+jupyter-console==6.0.0
+jupyter-core==4.5.0
kiwisolver==1.1.0
-m2r==0.2.1
MarkupSafe==1.1.1
-matplotlib==3.1.2
+matplotlib==3.1.1
mistune==0.8.4
-numpy==1.17.4
-packaging==19.2
-pandas==0.25.3
+multiprocess==0.70.9
+nbconvert==5.6.0
+nbformat==4.4.0
+notebook==6.0.0
+numpy==1.17.0
+pandas==0.25.0
+pandocfilters==1.4.2
parso==0.5.1
+pathos==0.2.5
pexpect==4.7.0
pickleshare==0.7.5
-prompt-toolkit==2.0.10
+pox==0.2.7
+ppft==1.6.6.1
+prometheus-client==0.7.1
+prompt-toolkit==2.0.9
ptyprocess==0.6.0
Pygments==2.4.2
-pyparsing==2.4.5
-python-dateutil==2.8.1
-pytz==2019.3
-requests==2.22.0
-six==1.13.0
-snowballstemmer==2.0.0
-Sphinx==2.2.1
-sphinx-rtd-theme==0.4.3
-sphinxcontrib-applehelp==1.0.1
-sphinxcontrib-devhelp==1.0.1
-sphinxcontrib-htmlhelp==1.0.2
-sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.2
-sphinxcontrib-serializinghtml==1.1.3
-traitlets==4.3.3
-urllib3==1.25.7
+pyparsing==2.4.2
+pyrsistent==0.15.4
+python-dateutil==2.8.0
+pytz==2019.2
+pyzmq==18.1.0
+qtconsole==4.5.2
+Send2Trash==1.5.0
+six==1.12.0
+terminado==0.8.2
+testpath==0.4.2
+tornado==6.0.3
+traitlets==4.3.2
wcwidth==0.1.7
+webencodings==0.5.1
+widgetsnbextension==3.5.1
diff --git a/tests/population/multiprocessing_via_population_comparison.py b/tests/population/multiprocessing_via_population_comparison.py
index 8b49b69c7..f8d466797 100644
--- a/tests/population/multiprocessing_via_population_comparison.py
+++ b/tests/population/multiprocessing_via_population_comparison.py
@@ -103,9 +103,9 @@ test_pop.set(separation=1000000000,
metallicity=0.002,
data_dir=os.path.join(os.environ['BINARYC_DATA_ROOT'], 'testing_python', 'multiprocessing2', name_testcase))
-# res = test_pop.evolve_population_comparison(parse_function, amt=int(amt_systems), nodes=int(amt_nodes))
-# with open('comparison_result.dat', 'a') as f:
-# f.write(str(res)+'\n')
+res = test_pop.evolve_population_comparison(parse_function, amt=int(amt_systems), nodes=int(amt_nodes))
+with open('comparison_result.dat', 'a') as f:
+ f.write(str(res)+'\n')
diff --git a/tests/population/surreypc_errorlog.txt b/tests/population/surreypc_errorlog.txt
new file mode 100644
index 000000000..14a6f1e78
--- /dev/null
+++ b/tests/population/surreypc_errorlog.txt
@@ -0,0 +1,42 @@
+adding: C_logging_code=
+if(stardata->star[0].SN_type != SN_NONE)
+{
+ if (stardata->model.time < stardata->model.max_evolution_time)
+ {
+ Printf("DAVID_SN %30.12e %g %g %g %d\n",
+ //
+ stardata->model.time, // 1
+ stardata->star[0].mass, //2
+ stardata->previous_stardata->star[0].mass, //3
+ stardata->star[0].pms_mass, //4
+ stardata->star[0].SN_type //5
+ );
+ };
+ /* Kill the simulation to save time */
+ stardata->model.max_evolution_time = stardata->model.time - stardata->model.dtm;
+};
+ to grid_options
+adding: separation=1000000000 to BSE_options
+adding: orbital_period=400000000 to BSE_options
+adding: metallicity=0.002 to BSE_options
+!! Key doesnt match previously known parameter: adding: data_dir=/vol/ph/astro_code/dhendriks/binaryc/results/testing_python/multiprocessing2/surreypc to custom_options
+/usr/bin/ld: /tmp/ccca3KKm.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
+/tmp/ccca3KKm.o: error adding symbols: Bad value
+collect2: error: ld returned 1 exit status
+Traceback (most recent call last):
+ File "multiprocessing_via_population_comparison.py", line 106, in <module>
+ res = test_pop.evolve_population_comparison(parse_function, amt=int(amt_systems), nodes=int(amt_nodes))
+ File "/vol/ph/astro_code/dhendriks/binaryc/binary_c-python/binarycpython/utils/grid.py", line 456, in evolve_population_comparison
+ self.set_custom_logging()
+ File "/vol/ph/astro_code/dhendriks/binaryc/binary_c-python/binarycpython/utils/grid.py", line 364, in set_custom_logging
+ ] = create_and_load_logging_function(custom_logging_code)
+ File "/vol/ph/astro_code/dhendriks/binaryc/binary_c-python/binarycpython/utils/custom_logging_functions.py", line 302, in create_and_load_logging_function
+ outfile_name=library_name,
+ File "/vol/ph/astro_code/dhendriks/binaryc/binary_c-python/binarycpython/utils/custom_logging_functions.py", line 262, in compile_shared_lib
+ res = subprocess.check_output("{command}".format(command=command), shell=True)
+ File "/user/HS128/dh00601/.pyenv/versions/3.6.4/lib/python3.6/subprocess.py", line 336, in check_output
+ **kwargs).stdout
+ File "/user/HS128/dh00601/.pyenv/versions/3.6.4/lib/python3.6/subprocess.py", line 418, in run
+ output=stdout, stderr=stderr)
+subprocess.CalledProcessError: Command 'gcc -DALIGNSIZE=8 -std=gnu99 -march=native -mtune=native -ffast-math -fno-associative-math -fno-finite-math-only -fsignaling-nans -fomit-frame-pointer -DCPUFREQ=3600 -DOPERATING_SYSTEM=linux -DLINUX -DPOSIX -DLARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DFPU_CONTROL -DGIT_REVISION=4797:20200127:369f3df -DGIT_URL=gitlab@gitlab.eps.surrey.ac.uk:ri0005/binary_c.git -D__HAVE_LIBC__ -D__HAVE_LIBGSL__ -I/user/HS128/dh00601/.local/include -DUSE_GSL -D__HAVE_LIBGSLCBLAS__ -D__HAVE_LIBBACKTRACE__ -D__HAVE_LIBBSD__ -D__HAVE_LIBM__ -D__HAVE_IEEE754_H__ -D__HAVE_DRAND48__ -D__HAVE_HSEARCH_DATA__ -D__HAVE_MALLOC_H__ -D__HAVE_SETITIMER__ -D__HAVE_PKG_CONFIG__ -D__HAVE_VALGRIND__ -D__SHOW_STARDATA__ -D__DIFF_STARDATA__ -O3 -shared -D_SEARCH_H -L/vol/ph/astro_code/dhendriks/binaryc/binary_c/src -L/user/HS128/dh00601/.local/lib -L/vol/ph/astro_code/dhendriks/binaryc/binary_c/src -lbinary_c -lc -lgsl -lgsl -lgslcblas -lm -lgslcblas -lbacktrace -lbsd -lm -o /tmp/binary_c_python/libcustom_logging_db727f25d8e14d4fbeaed42a32f23764.so /tmp/binary_c_python/custom_logging.c -I/vol/ph/astro_code/dhendriks/binaryc/binary_c -I/vol/ph/astro_code/dhendriks/binaryc/binary_c/src -I/usr/include -I/usr/local/include -I/vol/ph/astro_code/dhendriks/binaryc/binary_c/src' returned non-zero exit status 1.
+
diff --git a/tests/python_API_test.py b/tests/python_API_test.py
index ef1f1fbf5..6c79074ef 100755
--- a/tests/python_API_test.py
+++ b/tests/python_API_test.py
@@ -153,7 +153,7 @@ def test_run_system():
log_filename,
)
out = binary_c_python_api.run_system(argstring, -1, -1)
-
+ print(out)
####
if __name__ == "__main__":
--
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