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v-morello / pyne2001

A python wrapper around the original FORTRAN implementation of the NE2001 Galactic free electron density model
MIT License
2 stars 6 forks source link

error while loading shared libraries: libgfortran.so.3 #3

Closed tycohen closed 1 week ago

tycohen commented 3 weeks ago

After updating to RHEL8,

import pyne2001
pyne2001.test()
EEE.E.EE.EEEEE
======================================================================
ERROR: test_get_dist (test_pyne2001.TestFunctions)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/tests/test_pyne2001.py", line 14, in test_get_dist
    get_dist(0, 0, 400.0)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 202, in get_dist
    items = get_dist_full(glon, glat, dm)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 179, in get_dist_full
    return get_output(glon, glat, dm, 1)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 115, in get_output
    raise RuntimeError(msg)
RuntimeError: Failed to parse NE2001 output:
./NE2001: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

======================================================================
ERROR: test_get_dist_ffpe (test_pyne2001.TestFunctions)
Run get_dist() for a high Galactic latitude line of sight and
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/tests/test_pyne2001.py", line 54, in test_get_dist_ffpe
    get_dist(180.0, 80.0, 100.0)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 202, in get_dist
    items = get_dist_full(glon, glat, dm)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 179, in get_dist_full
    return get_output(glon, glat, dm, 1)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 115, in get_output
    raise RuntimeError(msg)
RuntimeError: Failed to parse NE2001 output:
./NE2001: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

======================================================================
ERROR: test_get_dist_full (test_pyne2001.TestFunctions)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/tests/test_pyne2001.py", line 17, in test_get_dist_full
    items = get_dist_full(0, 0, 400.0)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 179, in get_dist_full
    return get_output(glon, glat, dm, 1)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 115, in get_output
    raise RuntimeError(msg)
RuntimeError: Failed to parse NE2001 output:
./NE2001: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

======================================================================
ERROR: test_get_dm (test_pyne2001.TestFunctions)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/tests/test_pyne2001.py", line 8, in test_get_dm
    get_dm(0, 0, 10.0)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 158, in get_dm
    return get_dm_full(glon, glat, dist_kpc)['DM']
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 137, in get_dm_full
    return get_output(glon, glat, dist_kpc, -1)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 115, in get_output
    raise RuntimeError(msg)
RuntimeError: Failed to parse NE2001 output:
./NE2001: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

======================================================================
ERROR: test_get_dm_ffpe (test_pyne2001.TestFunctions)
Run get_dm() for a high Galactic latitude line of sight and
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/tests/test_pyne2001.py", line 45, in test_get_dm_ffpe
    get_dm(180.0, 80.0, 100.0)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 158, in get_dm
    return get_dm_full(glon, glat, dist_kpc)['DM']
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 137, in get_dm_full
    return get_output(glon, glat, dist_kpc, -1)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 115, in get_output
    raise RuntimeError(msg)
RuntimeError: Failed to parse NE2001 output:
./NE2001: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

======================================================================
ERROR: test_get_dm_full (test_pyne2001.TestFunctions)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/tests/test_pyne2001.py", line 11, in test_get_dm_full
    items = get_dm_full(0, 0, 10.0)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 137, in get_dm_full
    return get_output(glon, glat, dist_kpc, -1)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 115, in get_output
    raise RuntimeError(msg)
RuntimeError: Failed to parse NE2001 output:
./NE2001: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

======================================================================
ERROR: test_get_galactic_dm (test_pyne2001.TestFunctions)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/tests/test_pyne2001.py", line 20, in test_get_galactic_dm
    get_galactic_dm(0, 0)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 222, in get_galactic_dm
    return get_dm(glon, glat, 30.0)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 158, in get_dm
    return get_dm_full(glon, glat, dist_kpc)['DM']
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 137, in get_dm_full
    return get_output(glon, glat, dist_kpc, -1)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 115, in get_output
    raise RuntimeError(msg)
RuntimeError: Failed to parse NE2001 output:
./NE2001: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

======================================================================
ERROR: test_get_galactic_dm_anticentre (test_pyne2001.TestFunctions)
Check the numerical value of get_galactic_dm() for
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/tests/test_pyne2001.py", line 77, in test_get_galactic_dm_anticentre
    get_galactic_dm(180, 0),
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 222, in get_galactic_dm
    return get_dm(glon, glat, 30.0)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 158, in get_dm
    return get_dm_full(glon, glat, dist_kpc)['DM']
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 137, in get_dm_full
    return get_output(glon, glat, dist_kpc, -1)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 115, in get_output
    raise RuntimeError(msg)
RuntimeError: Failed to parse NE2001 output:
./NE2001: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

======================================================================
ERROR: test_get_galactic_dm_centre (test_pyne2001.TestFunctions)
Check the numerical value of get_galactic_dm() for
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/tests/test_pyne2001.py", line 68, in test_get_galactic_dm_centre
    get_galactic_dm(0, 0),
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 222, in get_galactic_dm
    return get_dm(glon, glat, 30.0)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 158, in get_dm
    return get_dm_full(glon, glat, dist_kpc)['DM']
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 137, in get_dm_full
    return get_output(glon, glat, dist_kpc, -1)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 115, in get_output
    raise RuntimeError(msg)
RuntimeError: Failed to parse NE2001 output:
./NE2001: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

======================================================================
ERROR: test_inversion1 (test_pyne2001.TestFunctions)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/tests/test_pyne2001.py", line 26, in test_inversion1
    dm = get_dm(glon, glat, dist_kpc)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 158, in get_dm
    return get_dm_full(glon, glat, dist_kpc)['DM']
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 137, in get_dm_full
    return get_output(glon, glat, dist_kpc, -1)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 115, in get_output
    raise RuntimeError(msg)
RuntimeError: Failed to parse NE2001 output:
./NE2001: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

======================================================================
ERROR: test_inversion2 (test_pyne2001.TestFunctions)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/tests/test_pyne2001.py", line 34, in test_inversion2
    dist_kpc, __ = get_dist(glon, glat, dm)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 202, in get_dist
    items = get_dist_full(glon, glat, dm)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 179, in get_dist_full
    return get_output(glon, glat, dm, 1)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/pulsartwg/lib/python2.7/site-packages/pyne2001/core.py", line 115, in get_output
    raise RuntimeError(msg)
RuntimeError: Failed to parse NE2001 output:
./NE2001: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

----------------------------------------------------------------------
Ran 14 tests in 0.169s

FAILED (errors=11)
tycohen commented 3 weeks ago

Works if installed using the makefile

v-morello commented 3 weeks ago

Hi @tycohen, From the looks of it, your OS upgrade may have resulted in libgfortran changing location/version, hence the error you are seeing.

Works if installed using the makefile

Are you sure that it's the Makefile install that works specifically, or just the fact that you reinstalled the package, which resulted in the fortran source being rebuilt and thus linked against the proper libgfortran ?

If you haven't tried already, can you make a fresh Python environment and install via this command ? pip install -vvv --no-cache pyne2001

If the module doesn't run properly, you can post the output of the command above and we can have a look.

tycohen commented 3 weeks ago

I installed via pip install -vvv --no-cache pyne2001.

import pyne2001 
pyne2001.test()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-2-2de12f894534> in <module>
----> 1 pyne2001.test()

AttributeError: module 'pyne2001' has no attribute 'test'
v-morello commented 3 weeks ago

Strange, but I can't help you unless you post the output of the above pip install command

tycohen commented 3 weeks ago 
Created temporary directory: /tmp/pip-ephem-wheel-cache-BWyy2u
Created temporary directory: /tmp/pip-req-tracker-t87tXL
Created requirements tracker '/tmp/pip-req-tracker-t87tXL'
Created temporary directory: /tmp/pip-install-1Gop3i
1 location(s) to search for versions of pyne2001:
* https://pypi.org/simple/pyne2001/
Getting page https://pypi.org/simple/pyne2001/
Found index url https://pypi.org/simple
Starting new HTTPS connection (1): pypi.org:443
https://pypi.org:443 "GET /simple/pyne2001/ HTTP/1.1" 200 609
Analyzing links from page https://pypi.org/simple/pyne2001/
  Found link https://files.pythonhosted.org/packages/43/d2/2ac1f40ae77414917ebdb714097c50e8ce9e4a798d4bdaed870a447a577b/pyne2001-0.1.1rc1.tar.gz#sha256=7d66882144ddb1ff95e07e9cfc6336518d587046cbc00f478efac8ea78f6893f (from https://pypi.org/simple/pyne2001/), version: 0.1.1rc1
  Found link https://files.pythonhosted.org/packages/45/89/99da82cb5c706e3d6933507a682ba95d1f7a2d7bc787ad71661c46780aef/pyne2001-0.1.1.tar.gz#sha256=08333294c71096e98e4e8eb0135ad46574cfc419748b09ca1d36203757e351b5 (from https://pypi.org/simple/pyne2001/), version: 0.1.1
  Found link https://files.pythonhosted.org/packages/73/02/d1daf549cc1721ce2e1c4760f0d5250905b8554e27aa28efe9e289ea5e9e/pyne2001-0.1.2.tar.gz#sha256=d7b9a158c657243ead602202af71cad7d4f7734946b0bfbdd953ab125d4e9081 (from https://pypi.org/simple/pyne2001/), version: 0.1.2
  Found link https://files.pythonhosted.org/packages/d8/d1/7a2a2a83091416e73fe43b1413dea1c842ea06438431545b315d7e1cfd76/pyne2001-0.1.3.tar.gz#sha256=a566c07e3bd8154b10f849e647f537bcbf52a9558fb8e6734bc2da88830d3433 (from https://pypi.org/simple/pyne2001/), version: 0.1.3
Given no hashes to check 3 links for project 'pyne2001': discarding no candidates
Using version 0.1.3 (newest of versions: 0.1.1, 0.1.2, 0.1.3)
Collecting pyne2001
  Created temporary directory: /tmp/pip-unpack-SlbFH0
  Starting new HTTPS connection (1): files.pythonhosted.org:443
  https://files.pythonhosted.org:443 "GET /packages/d8/d1/7a2a2a83091416e73fe43b1413dea1c842ea06438431545b315d7e1cfd76/pyne2001-0.1.3.tar.gz HTTP/1.1" 200 50050
  Downloading https://files.pythonhosted.org/packages/d8/d1/7a2a2a83091416e73fe43b1413dea1c842ea06438431545b315d7e1cfd76/pyne2001-0.1.3.tar.gz (50kB)
     |████████████████████████████████| 51kB 995kB/s 
  Added pyne2001 from https://files.pythonhosted.org/packages/d8/d1/7a2a2a83091416e73fe43b1413dea1c842ea06438431545b315d7e1cfd76/pyne2001-0.1.3.tar.gz#sha256=a566c07e3bd8154b10f849e647f537bcbf52a9558fb8e6734bc2da88830d3433 to build tracker '/tmp/pip-req-tracker-t87tXL'
    Running setup.py (path:/tmp/pip-install-1Gop3i/pyne2001/setup.py) egg_info for package pyne2001
    Running command python setup.py egg_info
    running egg_info
    creating /tmp/pip-install-1Gop3i/pyne2001/pip-egg-info/pyne2001.egg-info
    writing /tmp/pip-install-1Gop3i/pyne2001/pip-egg-info/pyne2001.egg-info/PKG-INFO
    writing top-level names to /tmp/pip-install-1Gop3i/pyne2001/pip-egg-info/pyne2001.egg-info/top_level.txt
    writing dependency_links to /tmp/pip-install-1Gop3i/pyne2001/pip-egg-info/pyne2001.egg-info/dependency_links.txt
    writing manifest file '/tmp/pip-install-1Gop3i/pyne2001/pip-egg-info/pyne2001.egg-info/SOURCES.txt'
    reading manifest file '/tmp/pip-install-1Gop3i/pyne2001/pip-egg-info/pyne2001.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no files found matching 'pyne2001/NE2001/bin/NE2001'
    warning: no files found matching 'pyne2001/NE2001/src/libNE2001.a'
    writing manifest file '/tmp/pip-install-1Gop3i/pyne2001/pip-egg-info/pyne2001.egg-info/SOURCES.txt'
  Source in /tmp/pip-install-1Gop3i/pyne2001 has version 0.1.3, which satisfies requirement pyne2001 from https://files.pythonhosted.org/packages/d8/d1/7a2a2a83091416e73fe43b1413dea1c842ea06438431545b315d7e1cfd76/pyne2001-0.1.3.tar.gz#sha256=a566c07e3bd8154b10f849e647f537bcbf52a9558fb8e6734bc2da88830d3433
  Removed pyne2001 from https://files.pythonhosted.org/packages/d8/d1/7a2a2a83091416e73fe43b1413dea1c842ea06438431545b315d7e1cfd76/pyne2001-0.1.3.tar.gz#sha256=a566c07e3bd8154b10f849e647f537bcbf52a9558fb8e6734bc2da88830d3433 from build tracker '/tmp/pip-req-tracker-t87tXL'
Building wheels for collected packages: pyne2001
  Created temporary directory: /tmp/pip-wheel-F5AlUM
  Building wheel for pyne2001 (setup.py) ...   Destination directory: /tmp/pip-wheel-F5AlUM
  Running command /lustre/aoc/students/tcohen/miniconda3/envs/testne2001/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1Gop3i/pyne2001/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1Gop3i/pyne2001/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-F5AlUM --python-tag cp27
  running bdist_wheel
  running build
  running build_py
  rm -f ../bin/NE2001 NE2001.o dmdsm.NE2001.o density.NE2001.o neLISM.NE2001.o neclumpN.o nevoidN.o scattering98.o libNE2001.a
  f77 -O -std=gnu  -c -o NE2001.o NE2001.f
  make: f77: Command not found
  make: *** [<builtin>: NE2001.o] Error 127
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/tmp/pip-install-1Gop3i/pyne2001/setup.py", line 97, in <module>
      'build_py': CustomBuildPy
    File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/site-packages/setuptools/__init__.py", line 145, in setup
      return distutils.core.setup(**attrs)
    File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/distutils/core.py", line 151, in setup
      dist.run_commands()
    File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/distutils/dist.py", line 953, in run_commands
      self.run_command(cmd)
    File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/site-packages/wheel/bdist_wheel.py", line 299, in run
      self.run_command('build')
    File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/distutils/cmd.py", line 326, in run_command
      self.distribution.run_command(command)
    File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/distutils/command/build.py", line 127, in run
      self.run_command(cmd_name)
    File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/distutils/cmd.py", line 326, in run_command
      self.distribution.run_command(command)
    File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/tmp/pip-install-1Gop3i/pyne2001/setup.py", line 49, in run
      compile_ne2001()
    File "/tmp/pip-install-1Gop3i/pyne2001/setup.py", line 17, in compile_ne2001
      subprocess.check_call('make all', shell=True)
    File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/subprocess.py", line 190, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command 'make all' returned non-zero exit status 2
error
  ERROR: Failed building wheel for pyne2001
  Running setup.py clean for pyne2001
  Running command /lustre/aoc/students/tcohen/miniconda3/envs/testne2001/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1Gop3i/pyne2001/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1Gop3i/pyne2001/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
  running clean
  'build/lib' does not exist -- can't clean it
  'build/bdist.linux-x86_64' does not exist -- can't clean it
  'build/scripts-2.7' does not exist -- can't clean it
Failed to build pyne2001
Installing collected packages: pyne2001
  Created temporary directory: /tmp/pip-record-08rKIC
    Running command /lustre/aoc/students/tcohen/miniconda3/envs/testne2001/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1Gop3i/pyne2001/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1Gop3i/pyne2001/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-08rKIC/install-record.txt --single-version-externally-managed --compile
    Running setup.py install for pyne2001 ...     running install
    rm -f ../bin/NE2001 NE2001.o dmdsm.NE2001.o density.NE2001.o neLISM.NE2001.o neclumpN.o nevoidN.o scattering98.o libNE2001.a
    f77 -O -std=gnu  -c -o NE2001.o NE2001.f
    make: f77: Command not found
    make: *** [<builtin>: NE2001.o] Error 127
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-1Gop3i/pyne2001/setup.py", line 97, in <module>
        'build_py': CustomBuildPy
      File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/site-packages/setuptools/__init__.py", line 145, in setup
        return distutils.core.setup(**attrs)
      File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/distutils/core.py", line 151, in setup
        dist.run_commands()
      File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/tmp/pip-install-1Gop3i/pyne2001/setup.py", line 27, in run
        compile_ne2001()
      File "/tmp/pip-install-1Gop3i/pyne2001/setup.py", line 17, in compile_ne2001
        subprocess.check_call('make all', shell=True)
      File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/subprocess.py", line 190, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command 'make all' returned non-zero exit status 2
error
Cleaning up...
  Removing source in /tmp/pip-install-1Gop3i/pyne2001
Removed build tracker '/tmp/pip-req-tracker-t87tXL'
ERROR: Command errored out with exit status 1: /lustre/aoc/students/tcohen/miniconda3/envs/testne2001/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1Gop3i/pyne2001/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1Gop3i/pyne2001/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-08rKIC/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
Exception information:
Traceback (most recent call last):
  File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/site-packages/pip/_internal/cli/base_command.py", line 153, in _main
    status = self.run(options, args)
  File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/site-packages/pip/_internal/commands/install.py", line 455, in run
    use_user_site=options.use_user_site,
  File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/site-packages/pip/_internal/req/__init__.py", line 62, in install_given_reqs
    **kwargs
  File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/site-packages/pip/_internal/req/req_install.py", line 888, in install
    cwd=self.unpacked_source_directory,
  File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/site-packages/pip/_internal/utils/subprocess.py", line 275, in runner
    spinner=spinner,
  File "/lustre/aoc/students/tcohen/miniconda3/envs/testne2001/lib/python2.7/site-packages/pip/_internal/utils/subprocess.py", line 242, in call_subprocess
    raise InstallationError(exc_msg)
InstallationError: Command errored out with exit status 1: /lustre/aoc/students/tcohen/miniconda3/envs/testne2001/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1Gop3i/pyne2001/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1Gop3i/pyne2001/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-08rKIC/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
1 location(s) to search for versions of pip:
* https://pypi.org/simple/pip/
Getting page https://pypi.org/simple/pip/
Found index url https://pypi.org/simple
Starting new HTTPS connection (1): pypi.org:443
https://pypi.org:443 "GET /simple/pip/ HTTP/1.1" 200 28933
Analyzing links from page https://pypi.org/simple/pip/
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v-morello commented 3 weeks ago

f77 -O -std=gnu -c -o NE2001.o NE2001.f make: f77: Command not found

There's the issue: the default fortran compiler on your system is f77 but it's not installed. Indeed if you look at the Makefile for the fortran source code here: https://github.com/v-morello/pyne2001/blob/master/pyne2001/NE2001/src/Makefile

You'll see that the fortran compiler is referred to via $(FC), which means the default fortran compiler on your system, and somehow that refers to something that isn't there. I'd assume that gfortran is the compiler that ships with most linux distros anyway.

I'd try and fix that by reinstalling gfortran and making sure it's in the $PATH. You may also want to try overriding the $FC env variable by doing this below, but it's not the "clean" solution:

FC=gfortran pip install pyne2001

Let me know how you get on, and then I'll close this because this is clearly not a pyne2001 issue.