I am struggling to compile the Planck likelihood and CosmoMC in my own desktop. I used to use CosmoMC on Sciama (which is a cluster) and there is no problem for that. However, when I try to install it on local, there are bunch of dependency problem.
I use Ubuntu 18.04, have just install intel parallel studio xe 2019 update2 cluster edition. I also download some other requirements like open mpi, cfitsio, fftw, gsl, and have them installed at /home/hanyu/SOFTWARE NAME/.
First I fellow https://cosmologist.info/cosmomc/readme_planck.html to set up the planck likelihood, I use
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hanyu@hanyus-ubuntu:~/plc-2.0$ ./waf configure --lapack_mkl=${MKLROOT} --cfitsio_prefix=/home/hanyu/cfitsio --install_all_deps
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mpif90 -mkl -O3 -no-prec-div -fpp -qopenmp -xHost -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/hanyu/plc-2.0/include -module ReleaseMPI -IReleaseMPI/ -c cliklike.f90 -o ReleaseMPI/cliklike.o
cliklike.f90(2): error #7013: This module file was not generated by any release of this compiler. [CLIK]
use clik
--------^
then this is what I got (sorry for the length)In file waf_tools/try_icc.py, line 32, replace -openmp by -qopenmp
In file waf_tools/try_ifort.py line 56, replace -openmp by -qopenmp
In file waf_tools/c_openmp.py line 28, replace -fopenmp by -qopenmp
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hanyu@hanyus-ubuntu:~/plc-2.0$ ./waf clean
add plik/component_plugin/rel2015/fg2015.c
add plik/component_plugin/rel2015/corrnoise.c
add plik/component_plugin/rel2015/leakage.c
'clean' finished successfully (0.013s)
hanyu@hanyus-ubuntu:~/plc-2.0$ ./waf configure --install_all_deps --lapack_mkl=${MKLROOT} --icc --ifort --cfitsio_prefix=/home/hanyu/cfitsio
Setting top to : /home/hanyu/plc-2.0
Setting out to : /home/hanyu/plc-2.0/build
Checking for program 'icc, ICL' : /home/hanyu/intel/compilers_and_libraries_2019.2.187/linux/bin/intel64/icc
Checking for program 'ar' : /usr/bin/ar
Compile a test code with icc : yes
retrieve icc link line : ok
icc link line :
Setting architecture flag to : -m64
Checking for $CC option to support OpenMP : -qopenmp
Checking for program 'ifort' : /home/hanyu/intel/compilers_and_libraries_2019.2.187/linux/bin/intel64/ifort
Checking for program 'xiar' : /usr/bin/ar
Check ifort version : 19.0.2.187
Compile a test code with ifort : yes
retrieve ifort link line : ok
fortran link line : -L/lib -L/lib64 -lirc -lpthread
Setting install root to : /home/hanyu/plc-2.0
Setting install bin directory to : /home/hanyu/plc-2.0/bin
Setting install lib directory to : /home/hanyu/plc-2.0/lib
Setting install include directory to : /home/hanyu/plc-2.0/include
Checking for program 'python' : /usr/bin/python
Checking for python version : 2.7.15
python-config : /usr/bin/python-config
Asking python-config for pyembed '--cflags --libs --ldflags' flags : yes
Getting pyembed flags from python-config : yes
Checking for library dl : yes
checking for RTLD_DEFAULT in dl : no
Checking for program 'pmc-config' : not found
Checking for library pmc : not found
Check mkl version : 10.3
create specific mkl lib : /home/hanyu/plc-2.0/lib/libclik_mkl.so
Checking for library ['clik_mkl', 'iomp5', 'pthread', 'm'] : yes
Checking for function dposv : yes
Checking for function dtrsv : yes
Checking for function dpotrf : yes
Checking for function dpotrs : yes
Checking for function dpotri : yes
Checking for function dtrtri : yes
Checking for function dtrmm : yes
Checking for function dtrmv : yes
Checking for function dgeqrf : yes
Checking for function dormqr : yes
Checking for function dsyev : yes
Checking for function dgesvd : yes
Checking for function dsymv : yes
Checking for function dgemv : yes
Checking for function dgemm : yes
Checking for function dsyrk : yes
Checking for function dsyr2k : yes
Checking for function daxpy : yes
Checking for function dtrsm : yes
Checking for function dsymm : yes
Checking for function dsyr : yes
Checking for function ddot : yes
Checking for function dsyevd : yes
Checking for function dlamch : yes
Checking for function dsyevr : yes
Checking for library ['cfitsio'] : yes
Checking for function fits_init_cfitsio : yes
Checking python module 'numpy' : ok
Checking python module 'pyfits' : ok
Checking python module 'cython' : ok
Checking python module 'cython' : ok
Checking cython version (>0.12) : 0.26.1
Checking for program 'cython' : /usr/bin/cython
Add plugin : 'rel2015' : ok
*----------------------------------------------------*
| |
| Configure step ok. |
| |
| run './waf install' now ! |
| |
*----------------------------------------------------*
'configure' finished successfully (5.464s)
hanyu@hanyus-ubuntu:~/plc-2.0$ ./waf install
Waf: Entering directory `/home/hanyu/plc-2.0/build'
add plik/component_plugin/rel2015/fg2015.c
add plik/component_plugin/rel2015/corrnoise.c
add plik/component_plugin/rel2015/leakage.c
[ 3/125] Processing src/gibbs/comm_br_mod.f90
[ 4/125] Processing src/gibbs/comm_gauss_br_mod.f90
[ 5/125] Processing src/lowlike/Planck_options.F90
[ 6/125] Processing src/cmbonly/plik_cmbonly.f90
- install /home/hanyu/plc-2.0/include/clik_lensing.h (from src/clik_lensing.h)
[ 6/125] Processing src/camspec/CAMspec.f90
[ 8/125] Processing src/clik.F90
- install /home/hanyu/plc-2.0/include/clik.h (from src/clik.h)
[ 6/125] Processing src/gibbs/comm_lowl_mod_dist.f90
- install /home/hanyu/plc-2.0/include/errorlist.h (from src/minipmc/errorlist.h)
[ 9/125] Processing src/bflike/healpix_types.f90
[ 10/125] Compiling src/lowlike/read_archive_map.f90
[ 11/125] Compiling src/lowlike/read_fits.f90
[ 12/125] Processing src/lowlike/br_mod_dist.f90
[ 13/125] Compiling src/python/clik/lkl.pyx
[ 14/125] Compiling src/python/clik/lkl_lensing.pyx
[ 15/125] Compiling src/python/clik/parametric.pyx
[ 16/125] Compiling src/plik/component_plugin/rel2015/rel2015.pyx
[ 17/125] Compiling src/python/clik/parobject.py
[ 18/125] Compiling src/python/clik/parobject.py
[ 19/125] Compiling src/python/clik/__init__.py
[ 20/125] Compiling src/python/clik/__init__.py
[ 21/125] Compiling src/python/clik/miniparse.py
[ 22/125] Compiling src/python/clik/miniparse.py
[ 23/125] Compiling src/python/clik/smicahlp.py
[ 24/125] Compiling src/python/clik/smicahlp.py
warning: /home/hanyu/plc-2.0/src/python/clik/lkl.pyx:4:8: 'stdlib' is deprecated, use 'libc.stdlib'
warning: /home/hanyu/plc-2.0/src/python/clik/lkl.pyx:5:8: 'stdio' is deprecated, use 'libc.stdio'
warning: /home/hanyu/plc-2.0/src/python/clik/lkl.pyx:49:13: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /home/hanyu/plc-2.0/src/python/clik/lkl.pyx:49:19: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /home/hanyu/plc-2.0/src/python/clik/lkl.pyx:207:13: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /home/hanyu/plc-2.0/src/python/clik/lkl.pyx:207:19: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
[ 25/125] Compiling src/python/clik/hpy.py
[ 26/125] Compiling src/python/clik/hpy.py
[ 27/125] Compiling src/python/clik/cldf.py
[ 28/125] Compiling src/python/clik/cldf.py
warning: /home/hanyu/plc-2.0/src/python/clik/lkl_lensing.pyx:4:8: 'stdlib' is deprecated, use 'libc.stdlib'
warning: /home/hanyu/plc-2.0/src/python/clik/lkl_lensing.pyx:5:8: 'stdio' is deprecated, use 'libc.stdio'
warning: /home/hanyu/plc-2.0/src/python/clik/lkl_lensing.pyx:51:13: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /home/hanyu/plc-2.0/src/python/clik/lkl_lensing.pyx:51:19: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /home/hanyu/plc-2.0/src/python/clik/lkl_lensing.pyx:150:13: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /home/hanyu/plc-2.0/src/python/clik/lkl_lensing.pyx:150:19: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
[ 29/125] Compiling src/python/tools/clik_print.py
[ 30/125] Compiling src/python/tools/prepare_wmap.py
[ 31/125] Compiling src/python/tools/clik_explore_1d.py
[ 32/125] Compiling src/python/tools/clik_change_lrange.py
[ 33/125] Compiling src/python/tools/clik_example_py.py
[ 34/125] Compiling src/python/tools/clik_get_selfcheck.py
- install /home/hanyu/plc-2.0/share/clik/rel2015/tsz_143_eps0.50.dat (from src/plik/component_plugin/rel2015/tsz_143_eps0.50.dat)
- install /home/hanyu/plc-2.0/lib/python2.7/site-packages/src/python/clik/parobject.py (from src/python/clik/parobject.py)
- install /home/hanyu/plc-2.0/share/clik/rel2015/sz_x_cib_template.dat (from src/plik/component_plugin/rel2015/sz_x_cib_template.dat)
- install /home/hanyu/plc-2.0/lib/python2.7/site-packages/src/python/clik/__init__.py (from src/python/clik/__init__.py)
- install /home/hanyu/plc-2.0/share/clik/rel2015/ksz_fromcamspec.dat (from src/plik/component_plugin/rel2015/ksz_fromcamspec.dat)
- install /home/hanyu/plc-2.0/lib/python2.7/site-packages/src/python/clik/miniparse.py (from src/python/clik/miniparse.py)
- install /home/hanyu/plc-2.0/share/clik/rel2015/cib_1h_2h_100_353_Jsr-1_PS_2014_09.dat (from src/plik/component_plugin/rel2015/cib_1h_2h_100_353_Jsr-1_PS_2014_09.dat)
- install /home/hanyu/plc-2.0/lib/python2.7/site-packages/src/python/clik/smicahlp.py (from src/python/clik/smicahlp.py)
- install /home/hanyu/plc-2.0/share/clik/rel2015/sky_template_v15_F100_143_217_353.dat (from src/plik/component_plugin/rel2015/sky_template_v15_F100_143_217_353.dat)
- install /home/hanyu/plc-2.0/lib/python2.7/site-packages/src/python/clik/hpy.py (from src/python/clik/hpy.py)
- install /home/hanyu/plc-2.0/share/clik/rel2015/cnoise_F100_143_217_353_v17.dat (from src/plik/component_plugin/rel2015/cnoise_F100_143_217_353_v17.dat)
[ 42/125] Processing src/lowlike/Planck_teeebb_pixlike.F90
- install /home/hanyu/plc-2.0/lib/python2.7/site-packages/src/python/clik/cldf.py (from src/python/clik/cldf.py)
[ 43/125] Processing src/cmbonly/clik_cmbonly.f90
[ 44/125] Compiling src/clik_example_f90.f90
[ 45/125] Processing src/plik/clik_plik.f90
[ 46/125] Processing src/camspec/clik_CAMspec.F90
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/parobject.pyc (from build/src/python/clik/parobject.pyc)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/__init__.pyc (from build/src/python/clik/__init__.pyc)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/parobject.pyo (from build/src/python/clik/parobject.pyo)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/miniparse.pyc (from build/src/python/clik/miniparse.pyc)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/__init__.pyo (from build/src/python/clik/__init__.pyo)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/smicahlp.pyc (from build/src/python/clik/smicahlp.pyc)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/miniparse.pyo (from build/src/python/clik/miniparse.pyo)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/hpy.pyc (from build/src/python/clik/hpy.pyc)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/cldf.pyc (from build/src/python/clik/cldf.pyc)
+ install /home/hanyu/plc-2.0/bin/clik_print (from build/src/python/clik_print)
+ install /home/hanyu/plc-2.0/bin/prepare_wmap (from build/src/python/prepare_wmap)
+ install /home/hanyu/plc-2.0/bin/clik_explore_1d (from build/src/python/clik_explore_1d)
+ install /home/hanyu/plc-2.0/bin/clik_change_lrange (from build/src/python/clik_change_lrange)
+ install /home/hanyu/plc-2.0/bin/clik_example_py (from build/src/python/clik_example_py)
+ install /home/hanyu/plc-2.0/bin/clik_get_selfcheck (from build/src/python/clik_get_selfcheck)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/hpy.pyo (from build/src/python/clik/hpy.pyo)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/smicahlp.pyo (from build/src/python/clik/smicahlp.pyo)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/cldf.pyo (from build/src/python/clik/cldf.pyo)
warning: /home/hanyu/plc-2.0/src/python/clik/parametric.pyx:4:8: 'stdlib' is deprecated, use 'libc.stdlib'
warning: /home/hanyu/plc-2.0/src/python/clik/parametric.pyx:5:8: 'stdio' is deprecated, use 'libc.stdio'
[ 65/125] Compiling src/cmbonly/clik_cmbonly.c
[ 66/125] Compiling src/plik/clik_plik.c
[ 67/125] Compiling build/src/plik/component_plugin/rel2015/rel2015.pyx.c
[ 68/125] Compiling src/gibbs/clik_gibbs.c
[ 69/125] Compiling src/plik/component_plugin/rel2015/fg2015.c
[ 70/125] Compiling src/lenslike/plenslike/plenslike_dat_full.c
[ 71/125] Compiling src/minipmc/distribution.c
[ 72/125] Compiling src/lenslike/plenslike/plenslike_dat_quad.c
[ 73/125] Compiling src/lowly_common.c
[ 74/125] Compiling src/plik/clik_hfipack.c
[ 75/125] Compiling src/plik/smica.c
[ 76/125] Compiling src/lenslike/plenslike/qest.c
[ 77/125] Compiling build/src/python/clik/lkl.pyx.c
../src/minipmc/distribution.c(580): warning #266: function "dtrsv" declared implicitly
dtrsv(&uplo,&trans,&diag,&ing->ndim,ing->std,&ing->ndim,ing->tmp,&xinc);
^
[ 78/125] Compiling src/lenslike/plenslike/wignerd.c
[ 79/125] Compiling src/clik_helper.c
[ 80/125] Compiling build/src/python/clik/lkl_lensing.pyx.c
[ 81/125] Compiling src/lenslike/plenslike/plenslike_dat_mono.c
[ 82/125] Compiling src/bflike/clik_bflike.c
[ 83/125] Compiling src/plik/clik_parametric.c
[ 84/125] Compiling src/plik/component_plugin/rel2015/leakage.c
[ 85/125] Compiling src/clik_lensing.c
[ 86/125] Compiling src/clik.c
[ 87/125] Compiling src/clik_dic.c
../src/plik/smica.c(509): warning #266: function "daxpy" declared implicitly
daxpy(&sz,&done,rq_0,&one, rq, &one);
^
../src/plik/smica.c(552): warning #266: function "dsyr" declared implicitly
dsyr(&uplo, &mm, &done, A, &one, AAt, &mm);
^
../src/plik/smica.c(688): warning #266: function "daxpy" declared implicitly
daxpy(&m2,mpars + iq,AAt,&one, rq+m2*iq, &one);
^
../src/plik/smica.c(827): warning #266: function "dsymm" declared implicitly
dsymm(&side, &uplo, &nd, &m, &done, P, &nd, A, &nd, &dzero, Ab, &nd);
^
../src/plik/smica.c(842): warning #266: function "dgemm" declared implicitly
dgemm(&transa, &transb, &m, &m, &nd, &done, A, &nd, Ab, &nd, &done, rq+m2*iq, &m);
^
../src/plik/smica.c(1509): warning #266: function "dtrsm" declared implicitly
dtrsm(&side, &uplo, &trans, &diag, &nn, &nn, &done, rq, &nn, rq_hat, &nn);
^
[ 88/125] Compiling build/src/python/clik/parametric.pyx.c
[ 89/125] Compiling src/lklbs.c
[ 90/125] Compiling src/plik/component_plugin/rel2015/corrnoise.c
[ 91/125] Compiling src/lenslike/plenslike/plenslike_dat_qecl.c
[ 92/125] Compiling src/plik/clik_parametric_addon.c
In file included from /usr/include/python2.7/numpy/ndarrayobject.h(18),
from /usr/include/python2.7/numpy/arrayobject.h(4),
from src/python/clik/lkl.pyx.c(485):
/usr/include/python2.7/numpy/ndarraytypes.h(84): warning #2650: attributes ignored here
NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"),
^
In file included from /usr/include/python2.7/numpy/ndarraytypes.h(1809),
from /usr/include/python2.7/numpy/ndarrayobject.h(18),
from /usr/include/python2.7/numpy/arrayobject.h(4),
from src/python/clik/lkl.pyx.c(485):
/usr/include/python2.7/numpy/npy_1_7_deprecated_api.h(15): warning #1224: #warning directive: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
#warning "Using deprecated NumPy API, disable it by " \
^
src/python/clik/lkl.pyx.c(3805): warning #266: function "clik_get_extra_parameter_names_by_lkl" declared implicitly
__pyx_v_n_names = clik_get_extra_parameter_names_by_lkl(__pyx_v_self->celf, __pyx_v_ilkl, (&__pyx_v_names), __pyx_v_self->err);
^
[ 93/125] Processing src/gibbs/clik_gibbs.f90
[ 94/125] Compiling src/minipmc/io.c
[ 95/125] Compiling src/cldf/cldf.c
[ 96/125] Compiling src/minipmc/errorlist.c
../src/lklbs.c(332): warning #266: function "dgemv" declared implicitly
dgemv(&trans, &ndim, &npar, &done, llkl->bins, &ndim, cls, &one, &dzero, llkl->pls, &one);
^
[ 97/125] Compiling src/clik_example_c.c
[ 98/125] Compiling src/cldf/cfrd.c
../src/clik_example_c.c(45): warning #266: function "read_double_vector" declared implicitly
cl_and_pars = read_double_vector(argv[i],ndim,err);
^
../src/clik_example_c.c(45): warning #556: a value of type "int" cannot be assigned to an entity of type "double *"
cl_and_pars = read_double_vector(argv[i],ndim,err);
^
../src/clik_example_c.c(135): warning #266: function "read_double_vector" declared implicitly
cl_and_pars = read_double_vector(argv[i],ndim,err);
^
../src/clik_example_c.c(135): warning #556: a value of type "int" cannot be assigned to an entity of type "double *"
cl_and_pars = read_double_vector(argv[i],ndim,err);
^
[ 99/125] Compiling src/lowlike/clik_lowlike.c
[100/125] Compiling src/camspec/clik_CAMspec.c
[101/125] Compiling src/clik_fortran.c
[102/125] Processing src/bflike/long_intrinsic_smw.f90
[103/125] Processing src/lowlike/Planck_likelihood.F90
[104/125] Processing src/bflike/fitstools_smw.f90
[105/125] Processing src/lowlike/clik_lowlike.f90
In file included from /usr/include/python2.7/numpy/ndarrayobject.h(18),
from /usr/include/python2.7/numpy/arrayobject.h(4),
from src/python/clik/lkl_lensing.pyx.c(485):
/usr/include/python2.7/numpy/ndarraytypes.h(84): warning #2650: attributes ignored here
NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"),
^
In file included from /usr/include/python2.7/numpy/ndarraytypes.h(1809),
from /usr/include/python2.7/numpy/ndarrayobject.h(18),
from /usr/include/python2.7/numpy/arrayobject.h(4),
from src/python/clik/lkl_lensing.pyx.c(485):
/usr/include/python2.7/numpy/npy_1_7_deprecated_api.h(15): warning #1224: #warning directive: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
#warning "Using deprecated NumPy API, disable it by " \
^
[106/125] Processing src/bflike/bflike_smw.f90
[107/125] Processing src/bflike/bflike_QUonly.f90
[108/125] Processing src/bflike/bflike.f90
In file included from /usr/include/python2.7/numpy/ndarrayobject.h(18),
from /usr/include/python2.7/numpy/arrayobject.h(4),
from src/python/clik/parametric.pyx.c(487):
/usr/include/python2.7/numpy/ndarraytypes.h(84): warning #2650: attributes ignored here
NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"),
^
In file included from /usr/include/python2.7/numpy/ndarraytypes.h(1809),
from /usr/include/python2.7/numpy/ndarrayobject.h(18),
from /usr/include/python2.7/numpy/arrayobject.h(4),
from src/python/clik/parametric.pyx.c(487):
/usr/include/python2.7/numpy/npy_1_7_deprecated_api.h(15): warning #1224: #warning directive: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
#warning "Using deprecated NumPy API, disable it by " \
^
[109/125] Processing src/bflike/clik_bflike.f90
[110/125] Linking build/src/libclik.so
+ install /home/hanyu/plc-2.0/lib/libclik.so (from build/src/libclik.so)
[115/125] Linking build/src/python/parametric.so
[115/125] Linking build/src/python/lkl.so
[115/125] Linking build/src/python/rel2015.so
[115/125] Linking build/src/python/lkl_lensing.so
[116/125] Linking build/src/clik_example_C
[117/125] Linking build/src/libclik_f90.so
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/parametric.so (from build/src/python/parametric.so)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/rel2015.so (from build/src/python/rel2015.so)
+ install /home/hanyu/plc-2.0/lib/python2.7/site-packages/clik/lkl.so (from build/src/python/lkl.so)
src/libclik.so: undefined reference to `for_f90_index'
src/libclik.so: undefined reference to `for_close'
src/libclik.so: undefined reference to `for_cpystr'
src/libclik.so: undefined reference to `for_allocate'
src/libclik.so: undefined reference to `for_backspace'
src/libclik.so: undefined reference to `for_concat'
src/libclik.so: undefined reference to `for_read_int_fmt'
src/libclik.so: undefined reference to `for_dealloc_allocatable'
src/libclik.so: undefined reference to `for_deallocate_all'
src/libclik.so: undefined reference to `for_read_seq'
src/libclik.so: undefined reference to `for_cpstr'
src/libclik.so: undefined reference to `for_alloc_allocatable'
src/libclik.so: undefined reference to `for_open'
src/libclik.so: undefined reference to `for_read_seq_fmt'
src/libclik.so: undefined reference to `for_deallocate'
src/libclik.so: undefined reference to `for_len_trim'
src/libclik.so: undefined reference to `for_realloc_lhs'
src/libclik.so: undefined reference to `for_array_copy_in'
src/libclik.so: undefined reference to `for_rewind'
src/libclik.so: undefined reference to `for_trim'
src/libclik.so: undefined reference to `for_read_int_lis'
src/libclik.so: undefined reference to `for_stop_core'
src/libclik.so: undefined reference to `for_cpusec_t'
src/libclik.so: undefined reference to `for_read_seq_lis'
src/libclik.so: undefined reference to `for_write_seq'
src/libclik.so: undefined reference to `for_inquire'
src/libclik.so: undefined reference to `for_contig_array'
src/libclik.so: undefined reference to `for_read_seq_lis_xmit'
src/libclik.so: undefined reference to `for_check_mult_overflow64'
src/libclik.so: undefined reference to `for_write_seq_fmt_xmit'
src/libclik.so: undefined reference to `for_write_seq_fmt'
src/libclik.so: undefined reference to `for_array_copy_out'
src/libclik.so: undefined reference to `for_read_seq_xmit'
src/libclik.so: undefined reference to `for_write_seq_lis_xmit'
src/libclik.so: undefined reference to `for_write_seq_lis'
src/libclik.so: undefined reference to `for_read_int_lis_xmit'
src/libclik.so: undefined reference to `for_adjustl'
src/libclik.so: undefined reference to `for_read_seq_nml'
src/libclik.so: undefined reference to `for_exit'
Waf: Leaving directory `/home/hanyu/plc-2.0/build'
Build failed
-> task in 'clik_example_C' failed (exit status 1):
{task 139701496146064: cprogram clik_example_c.c.7.o -> clik_example_C}
['/home/hanyu/intel/compilers_and_libraries_2019.2.187/linux/bin/intel64/icc', '-m64', 'src/clik_example_c.c.7.o', '-o', '/home/hanyu/plc-2.0/build/src/clik_example_C', '-Wl,-rpath,/lib', '-Wl,-rpath,/lib64', '-Wl,-rpath,/home/hanyu/plc-2.0/lib', '-Wl,-rpath,/home/hanyu/plc-2.0/lib', '-Wl,-rpath,/lib', '-Wl,-rpath,/lib64', '-Wl,-rpath,/home/hanyu/cfitsio/lib', '-Wl,-rpath,/lib', '-Wl,-rpath,/lib64', '', '', '-L/lib', '-L/lib64', '-Lsrc', '-L/home/hanyu/plc-2.0/lib', '-L/lib', '-L/lib64', '-L/home/hanyu/cfitsio/lib', '-L/lib', '-L/lib64', '-lpthread', '-lclik', '-lclik_mkl', '-liomp5', '-lpthread', '-lm', '-ldl', '-lcfitsio', '-lirc', '-lpthread']
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20 # set the path of the cfitsio lib.
21 # bewared that cfitsio must have been compiled with the option "make shared"
22 CFITSIOPATH := /home/hanyu/cfitsio
23 #CFITSIOPATH := /softs/cfitsio/3.24
24 # you have a CFITSIO lib in a weird location, also set those
25 CFITSIO_INCPATH := $(CFITSIOPATH)/include
26 CFITSIO_LIBPATH := $(CFITSIOPATH)/lib
27
28 #define your compilers and stuff
29 CC = icc
30 FC = ifort
31
32 # ifort
33 # if you are using ifort set here where its lib are installed
34 # and check the runtime libs
35 # PLEASE note that gcc 4.9 and ifort <14.0.4 have an imcompativbility
36 # (see https://software.intel.com/en-us/articles/gcc-49-openmp-code-cannot-b e-linked-with-intel-openmp-runtime)
37
38 # on my mac I got
39 #IFORTLIBPATH = /usr/bin/ifort-2011-base/compiler/lib
40 #IFORTRUNTIME = -L$(IFORTLIBPATH) -lintlc -limf -lsvml -liomp5 -lifportmt -l ifcoremt -lpthread
41
42 # on a linux machine, ifort 11.1
43 #IFORTLIBPATH = /softs/intel/fce/11.1.075/lib/intel64
44 #IFORTRUNTIME = -L$(IFORTLIBPATH) -lintlc -limf -lsvml -liomp5 -lifport -lif coremt -lpthread
45
46 # on a linux machine, ifort 14.0
47 IFORTLIBPATH = /home/hanyu/intel/compilers_and_libraries_2019.2.187/linux/bi n/intel64
48 IFORTRUNTIME = -L$(IFORTLIBPATH) -lintlc -limf -lsvml -liomp5 -lifport -lifc oremt -lirc -lpthread
49
50 # gfortran
51 # if you are using gfortran set here where the lib are installed
52 # and check the runtime libs
53 GFORTRANLIBPATH = /usr/lib
54 GFORTRANRUNTIME = -L$(GFORTRANLIBPATH) -lgfortran -lgomp
55
56 # if you are on linux and using mkl, you need to set this
57 MKLROOT = /home/hanyu/intel/compilers_and_libraries_2019.2.187/linux/mkl
58 LAPACKLIBPATHMKL = -L$(MKLROOT)/lib/intel64
59 #some example
60 #MKLROOT = /softs/intel/mkl/10.2.6.038/
61 # on mkl 10.3
62 #LAPACKLIBPATHMKL = -L$(MKLROOT)/lib/intel64
63 # on mkl 10.2
64 #LAPACKLIBPATHMKL = -L$(MKLROOT)/lib/em64t
65
66 #if you want to point to your own version of lapack set the following variab les
67 #LAPACK = -L/some/path -lsomefortranlapack -lsomedependencyforyourlapack
68 #LAPACKLIBPATH = /some/path
69
70
71 # pretty colors (comment to remove pretty colors or try to change echo to ec ho -e)
72 COLORS = 1
73
74 #set echo to echo -e to have colourized output on some shell
75 ECHO = echo
76
77
78 # what is the openmp option for your C compiler (leave empty to cmpile witho ut openmp)
79 COPENMP = -qopenmp
80 # what is the openmp option for your F90 compiler (leave empty to cmpile wit hout openmp)
81 FOPENMP = -qopenmp
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\x1b[31;01mI suspect an error with your MKLROOT, or MKL_LIB_FULLPATH, please check\x1b[0m
build \x1b[36;11m/home/hanyu/plc-2.0/buildir/liblapack_clik.so \x1b[0m,
(see chapter 5 in http://software.intel.com/sites/products/documentation/hpc/mkl/lin/)
using the following command line:
gcc -shared -Bdynamic -u dposv_ -u dtrsv_ -u dpotrf_ -u dpotrs_ -u dpotri_ -u dtrtri_ -u dtrmm_ -u dtrmv_ -u dgeqrf_ -u dormqr_ -u dsyev_ -u dgesvd_ -u dsymv_ -u dgemv_ -u dgemm_ -u dsyrk_ -u dsyr2k_ -u daxpy_ -u dtrsm_ -u dsymm_ -u dsyr_ -u ddot_ -u dsyevd_ -u dlamch_ -u dsyevr_ -Wl,--start-group -Wl,--end-group -L/home/hanyu/intel/compilers_and_libraries_2019.2.187/linux/bin/intel64 -L/lib -L/lib64 -liomp5 -lpthread -lm -o /home/hanyu/plc-2.0/buildir/liblapack_clik.so
build \x1b[36;11m/home/hanyu/plc-2.0/buildir/libclik.so \x1b[0m
\x1b[32;11msrc/clik_fortran.c \x1b[0m -> \x1b[32;11m /home/hanyu/plc-2.0/buildir/tmp/clik_fortran.o \x1b[0m
\x1b[32;11msrc/clik.F90 \x1b[0m -> \x1b[32;11m /home/hanyu/plc-2.0/buildir/tmp/clik.f90.o \x1b[0m
build \x1b[36;11m/home/hanyu/plc-2.0/buildir/libclik_f90.so \x1b[0m
\x1b[32;11msrc/clik_example_c.c \x1b[0m -> \x1b[32;11m /home/hanyu/plc-2.0/buildir/tmp/clik_example_c.o \x1b[0m
src/clik_example_c.c(45): warning #266: function "read_double_vector" declared implicitly
cl_and_pars = read_double_vector(argv[i],ndim,err);
^
src/clik_example_c.c(45): warning #556: a value of type "int" cannot be assigned to an entity of type "double *"
cl_and_pars = read_double_vector(argv[i],ndim,err);
^
src/clik_example_c.c(135): warning #266: function "read_double_vector" declared implicitly
cl_and_pars = read_double_vector(argv[i],ndim,err);
^
src/clik_example_c.c(135): warning #556: a value of type "int" cannot be assigned to an entity of type "double *"
cl_and_pars = read_double_vector(argv[i],ndim,err);
^
build \x1b[36;11m/home/hanyu/plc-2.0/buildir/clik_example_C \x1b[0m
icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dsymm_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dpotrf_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dgemm_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dpotri_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dtrsv_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dsyevr_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dpotrs_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dsyr_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dtrsm_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dsyevd_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `daxpy_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dsyrk_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `ddot_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dsymv_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dgemv_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dlamch_'
/home/hanyu/plc-2.0/buildir/libclik.so: undefined reference to `dposv_'
Makefile:346: recipe for target '/home/hanyu/plc-2.0/buildir/clik_example_C' failed
make: *** [/home/hanyu/plc-2.0/buildir/clik_example_C] Error 1
Finally, my .bashrc
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119 ###parallel studio####
120 source /home/hanyu/intel/compilers_and_libraries_2019.2.187/linux/bin/ifortvars .sh intel64
121 source /home/hanyu/intel/compilers_and_libraries_2019.2.187/linux/bin/iccvars.s h intel64
122 ###mpi###
123 PATH="/home/hanyu/openmpi/bin":${PATH}
124 export PATH
125
126 LD_LIBRARY_PATH="/home/hanyu/openmpi/lib":$LD_LIBRARY_PATH
127 export LD_LIBRARY_PATH
128 ###cfitsio###
129 export LD_LIBRARY_PATH=/home/hanyu/cfitsio/lib:${LD_LIBRARY_PATH}
130 ###fftw###
131 #export LD_LIBRARY_PATH=/home/hanyu/fftw/lib:${LD_LIBRARY_PATH}
132 ###gsl###
133 #export LD_LIBRARY_PATH=/home/hanyu/gsl/lib:${LD_LIBRARY_PATH}
134 ###PLK2.0###
135 export PLANCKLIKE=cliklike
136 export CLIK_PATH=/home/hanyu/plc-2.0
137 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CLIK_PATH/lib
138 #source $CLIK_PATH/bin/clik_profile.sh
139 ###mkl###
140 #export MKLROOT=/home/hanyu/intel/mkl:${MKLROOT}
141
142
143
144 source /home/hanyu/plc-2.0/bin/clik_profile.sh
145 export PYTHONPATH=/home/hanyu/projects/CosmoMC-Nov2016/python:$PYTHONPATH
Hanyu