CobraPy instalation not finding glpk.h

[Marcelo Melo]

Hello everyone,

I'm trying to install COBRApy in a cluster (Stampede) to do a large scale sweep of parameters, but I'm getting stuck on the installation.

The cluster already has GMP and GLPK installed, but in non standard locations  (/opt/apps/gcc4_7/glpk/4.45/).

I installed VirtualEnv so I could have my own python environment where I could install everything, and I did install PyGLPK from COBRA sourceforge package. It built with no errors, tested fine and installed also with no errors. The result is that I am able to load the module glpk (import glpk).

However, when I try to install cobra, I get several errors due to the setup process not finding glpk.h (the full output is below).

The header file is there, in the non-standard location. I checked:  /opt/apps/gcc4_7/glpk/4.45/include/glpk.h

Cobra finishes the instalation but apparently with no support for glpk.

Curiously, if I import glpk before importing cobra, then cobra finds it and is able to use it for optimization of models, even though the installation gives errors.

Is there anything I can do to direct the instalation process to look for the header file in the right place?

On a side note, if I run "pip install cobra", without the "--pre" at the end, it installs version 0.2.1 with no errors and is able to load glpk on its own.

Thank you for your attention.

Marcelo

##################  Full output of instalation.

(PyEnv)[user@login2 Programas]$ pip install cobra --pre  

Downloading/unpacking cobra

  Downloading cobra-0.3.0b2.tar.gz (2.2MB): 2.2MB downloaded

  Running setup.py (path:/home1/02603/user/Programas/PyEnv/build/cobra/setup.py) egg_info for package cobra

    ('missing cimport', 'cobra/solvers/cglpk.pyx')

    libc.stdlib

        glpk

    /opt/apps/python/epd/7.3.2/lib/python2.7/site-packages/Cython/Includes/libc/stdlib.pxd

    

Installing collected packages: cobra

  Running setup.py install for cobra

    ('missing cimport', 'cobra/solvers/cglpk.pyx')

    libc.stdlib

        glpk

    /opt/apps/python/epd/7.3.2/lib/python2.7/site-packages/Cython/Includes/libc/stdlib.pxd

    building 'cobra.solvers.cglpk' extension

    gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -fPIC -I/opt/apps/python/epd/7.3.2/include/python2.7 -c cobra/solvers/cglpk.c -o build/temp.linux-x86_64-2.7/cobra/solvers/cglpk.o

    cobra/solvers/cglpk.c:343:18: error: glpk.h: No such file or directory

    cobra/solvers/cglpk.c:547: error: expected specifier-qualifier-list before ‘glp_prob’

    cobra/solvers/cglpk.c:859: error: expected ‘)’ before ‘s’

    cobra/solvers/cglpk.c: In function ‘__pyx_pf_5cobra_7solvers_5cglpk_3GLP___cinit__’:

    cobra/solvers/cglpk.c:1205: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:1214: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:1214: error: ‘GLP_MAX’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:1214: error: (Each undeclared identifier is reported only once

    cobra/solvers/cglpk.c:1214: error: for each function it appears in.)

    cobra/solvers/cglpk.c:1223: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:1232: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘integer_parameters’

    cobra/solvers/cglpk.c: In function ‘__pyx_pf_5cobra_7solvers_5cglpk_3GLP_2__dealloc__’:

    cobra/solvers/cglpk.c:1278: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c: In function ‘__pyx_pf_5cobra_7solvers_5cglpk_3GLP_4__init__’:

    cobra/solvers/cglpk.c:1364: error: ‘glp_prob’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:1364: error: ‘__pyx_v_glp’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:1382: error: ‘__pyx_t_3’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:1411: error: ‘GLP_OFF’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:1420: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:1420: error: ‘GLP_MSG_ERR’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:1451: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:1701: error: ‘GLP_FX’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:1722: error: ‘GLP_UP’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:1743: error: ‘GLP_LO’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:1879: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:1879: error: ‘GLP_BV’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:1891: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:1891: error: ‘GLP_IV’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:1935: error: ‘GLP_DB’ undeclared (first use in this function)

    cobra/solvers/cglpk.c: In function ‘__pyx_f_5cobra_7solvers_5cglpk_3GLP_change_variable_bounds’:

    cobra/solvers/cglpk.c:2468: error: ‘GLP_DB’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:2503: error: ‘GLP_FX’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:2515: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c: In function ‘__pyx_pf_5cobra_7solvers_5cglpk_3GLP_10change_coefficient’:

    cobra/solvers/cglpk.c:2760: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:2813: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:2852: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:2892: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c: In function ‘__pyx_pf_5cobra_7solvers_5cglpk_3GLP_12solve_problem’:

    cobra/solvers/cglpk.c:2964: error: ‘glp_smcp’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:2964: error: expected ‘;’ before ‘__pyx_v_parameters’

    cobra/solvers/cglpk.c:2965: error: ‘glp_iocp’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:2965: error: expected ‘;’ before ‘__pyx_v_integer_parameters’

    cobra/solvers/cglpk.c:2966: error: ‘glp_prob’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:2966: error: ‘__pyx_v_glp’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:2971: error: expected ‘;’ before ‘__pyx_t_1’

    cobra/solvers/cglpk.c:2972: error: expected ‘;’ before ‘__pyx_t_2’

    cobra/solvers/cglpk.c:2973: error: ‘__pyx_t_3’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:2996: error: ‘__pyx_t_1’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:2996: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:2997: error: ‘__pyx_v_parameters’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:3006: error: ‘__pyx_t_2’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:3006: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘integer_parameters’

    cobra/solvers/cglpk.c:3007: error: ‘__pyx_v_integer_parameters’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:3016: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:3177: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:3178: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘integer_parameters’

    cobra/solvers/cglpk.c:3187: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:3188: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘integer_parameters’

    cobra/solvers/cglpk.c:3197: error: ‘GLP_OFF’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:3215: error: ‘GLP_ON’ undeclared (first use in this function)

    cobra/solvers/cglpk.c: In function ‘__pyx_pf_5cobra_7solvers_5cglpk_3GLP_16get_status’:

    cobra/solvers/cglpk.c:3497: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:3499: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:3510: error: ‘GLP_OPT’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:3533: error: ‘GLP_FEAS’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:3544: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:3558: error: ‘GLP_UNDEF’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:3581: error: ‘GLP_UNBND’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:3604: error: ‘GLP_NOFEAS’ undeclared (first use in this function)

    cobra/solvers/cglpk.c: In function ‘__pyx_f_5cobra_7solvers_5cglpk_3GLP_set_objective_sense’:

    cobra/solvers/cglpk.c:3728: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:3728: error: ‘GLP_MAX’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:3749: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:3749: error: ‘GLP_MIN’ undeclared (first use in this function)

    cobra/solvers/cglpk.c: In function ‘__pyx_f_5cobra_7solvers_5cglpk_3GLP_set_parameter’:

    cobra/solvers/cglpk.c:3939: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:3961: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:3971: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:3993: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:4015: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘integer_parameters’

    cobra/solvers/cglpk.c:4039: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘integer_parameters’

    cobra/solvers/cglpk.c:4075: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:4075: error: ‘GLP_MSG_ERR’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:4097: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:4097: error: ‘GLP_MSG_OFF’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:4124: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:4124: error: ‘GLP_MSG_ALL’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:4145: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘parameters’

    cobra/solvers/cglpk.c:4145: error: ‘GLP_MSG_ON’ undeclared (first use in this function)

    cobra/solvers/cglpk.c: In function ‘__pyx_f_5cobra_7solvers_5cglpk_3GLP_get_objective_value’:

    cobra/solvers/cglpk.c:4322: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:4337: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c: In function ‘__pyx_f_5cobra_7solvers_5cglpk_3GLP_change_variable_objective’:

    cobra/solvers/cglpk.c:4477: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c: In function ‘__pyx_f_5cobra_7solvers_5cglpk_3GLP_is_mip’:

    cobra/solvers/cglpk.c:4635: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c: In function ‘__pyx_pf_5cobra_7solvers_5cglpk_3GLP_28format_solution’:

    cobra/solvers/cglpk.c:4727: error: ‘glp_prob’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:4727: error: ‘__pyx_v_glp’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:4735: error: ‘__pyx_t_1’ undeclared (first use in this function)

    cobra/solvers/cglpk.c:4758: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c: In function ‘__pyx_pf_5cobra_7solvers_5cglpk_3GLP_30__getstate__’:

    cobra/solvers/cglpk.c:5382: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c: In function ‘__pyx_pf_5cobra_7solvers_5cglpk_3GLP_34__setstate__’:

    cobra/solvers/cglpk.c:5886: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c: In function ‘__pyx_pf_5cobra_7solvers_5cglpk_3GLP_36__copy__’:

    cobra/solvers/cglpk.c:6002: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:6002: error: ‘struct __pyx_obj_5cobra_7solvers_5cglpk_GLP’ has no member named ‘glp’

    cobra/solvers/cglpk.c:6002: error: ‘GLP_ON’ undeclared (first use in this function)

    cobra/solvers/cglpk.c: In function ‘initcglpk’:

    cobra/solvers/cglpk.c:7828: warning: passing argument 1 of ‘PyString_FromString’ makes pointer from integer without a cast

    /opt/apps/python/epd/7.3.2/include/python2.7/stringobject.h:63: note: expected ‘const char *’ but argument is of type ‘int’

    cobra/solvers/cglpk.c: At top level:

    cobra/solvers/cglpk.c:9241: error: expected ‘)’ before ‘s’

    

Successfully installed cobra

Cleaning up...

[Ali Ebrahim]

Hello Marcelo,

Even though error messages occurred during compilation of the included cglpk solver, it looks like the rest of the installation was still successful for the --pre version. If you have other solvers (such as pyGLPK, Gurobi, or cplex) already installed, it will work as expected even if you got error messages for cglpk. Therefore, if you have another solver (which it sounds like you do) in your virtual environment, I would just use cobrapy as it is, given that it functions just fine without cglpk.

If you want cglpk to work, you can edit build_args in setup.py to add to the include_dirs and library_dirs where glpk is installed (around https://github.com/opencobra/cobrapy/blob/master/setup.py#L66). Another way is to copy the .h and .a files to the same directory as setup.py. Still, I would recommend not going through too much trouble to install cglpk if you already have the regular glpk solver installed; it's there so that there is a solver compatible with the latest version of glpk (which pyglpk is not).

It looks like pyglpk does some "magic" to guess the glpk include/library directories by using which glpsol, which cobrapy doesn't do.

May I inquire what OS you are using?

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