I am trying to compile the plc-2.0 in a cluster. I did all the modifications mentioned in Added the lines
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export I_MPI_CC=icc
export I_MPI_CXX=icpc
export I_MPI_F77=ifort
export I_MPI_F90=ifort
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[narayan@dirac plc-2.0]$ mpif90 --version
ifort (IFORT) 19.0.1.144 20181018
Copyright (C) 1985-2018 Intel Corporation. All rights reserved.
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[narayan@dirac plc-2.0]$ ifort -V
Intel(R) Fortran Intel(R) 64 Compiler for applications running on Intel(R) 64, Version 19.0.1.144 Build 20181018
Copyright (C) 1985-2018 Intel Corporation. All rights reserved.
While configuring it shows ok.
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[narayan@dirac plc-2.0]$ ./waf configure --lapack_mkl=${MKLROOT} --install_all_deps --icc --ifort
Setting top to : /home/narayan/Cosmo_Programs/plc-2.0
Setting out to : /home/narayan/Cosmo_Programs/plc-2.0/build
Checking for program 'icc, ICL' : /home/softwares/intel/compilers_and_libraries_2019.1.144/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/softwares/intel/compilers_and_libraries_2019.1.144/linux/bin/intel64/ifort
Checking for program 'xiar' : /usr/bin/ar
Check ifort version : 19.0.1.144
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/narayan/Cosmo_Programs/plc-2.0
Setting install bin directory to : /home/narayan/Cosmo_Programs/plc-2.0/bin
Setting install lib directory to : /home/narayan/Cosmo_Programs/plc-2.0/lib
Setting install include directory to : /home/narayan/Cosmo_Programs/plc-2.0/include
Checking for program 'python' : /usr/bin/python
Checking for python version : 2.7.5
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/narayan/Cosmo_Programs/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) : 0.29.10
Checking for program 'cython' : /home/narayan/.local/bin/cython
Add plugin : 'rel2015' : ok
*----------------------------------------------------*
| |
| Configure step ok. |
| |
| run './waf install' now ! |
| |
*----------------------------------------------------*
'configure' finished successfully (8.186s)
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[narayan@dirac plc-2.0]$ ./waf install
Waf: Entering directory `/home/narayan/Cosmo_Programs/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/lowlike/Planck_options.F90
[ 2/125] Processing src/gibbs/comm_br_mod.f90
[ 5/125] Processing src/gibbs/comm_lowl_mod_dist.f90
[ 6/125] Processing src/cmbonly/plik_cmbonly.f90
[ 6/125] Processing src/camspec/CAMspec.f90
[ 6/125] Processing src/gibbs/comm_gauss_br_mod.f90
[ 10/125] Processing src/clik.F90
- install /home/narayan/Cosmo_Programs/plc-2.0/include/clik_lensing.h (from src/clik_lensing.h)
[ 10/125] Processing src/bflike/healpix_types.f90
[ 12/125] Compiling src/lowlike/read_archive_map.f90
[ 12/125] Compiling src/lowlike/read_fits.f90
[ 12/125] Processing src/lowlike/br_mod_dist.f90
- install /home/narayan/Cosmo_Programs/plc-2.0/include/clik.h (from src/clik.h)
[ 13/125] Compiling src/python/clik/lkl.pyx
- install /home/narayan/Cosmo_Programs/plc-2.0/include/errorlist.h (from src/minipmc/errorlist.h)
[ 14/125] Compiling src/python/clik/lkl_lensing.pyx
[ 15/125] Compiling src/python/clik/parametric.pyx
[ 19/125] Compiling src/plik/component_plugin/rel2015/rel2015.pyx
[ 19/125] Compiling src/python/clik/parobject.py
[ 20/125] Compiling src/python/clik/parobject.py
[ 20/125] Compiling src/python/clik/__init__.py
[ 22/125] Compiling src/python/clik/__init__.py
[ 22/125] Compiling src/python/clik/miniparse.py
[ 24/125] Compiling src/python/clik/miniparse.py
[ 25/125] Compiling src/python/clik/smicahlp.py
[ 26/125] Compiling src/python/clik/smicahlp.py
[ 27/125] Compiling src/python/clik/hpy.py
[ 26/125] Compiling src/python/clik/hpy.py
[ 29/125] Compiling src/python/clik/cldf.py
[ 29/125] Compiling src/python/clik/cldf.py
[ 29/125] Compiling src/python/tools/clik_change_lrange.py
[ 30/125] Compiling src/python/tools/clik_example_py.py
[ 32/125] Compiling src/python/tools/clik_get_selfcheck.py
[ 31/125] Compiling src/python/tools/clik_explore_1d.py
[ 34/125] Compiling src/python/tools/clik_print.py
[ 34/125] Compiling src/python/tools/prepare_wmap.py
- install /home/narayan/Cosmo_Programs/plc-2.0/share/clik/rel2015/tsz_143_eps0.50.dat (from src/plik/component_plugin/rel2015/tsz_143_eps0.50.dat)
- install /home/narayan/Cosmo_Programs/plc-2.0/share/clik/rel2015/sz_x_cib_template.dat (from src/plik/component_plugin/rel2015/sz_x_cib_template.dat)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/src/python/clik/__init__.py (from src/python/clik/__init__.py)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/src/python/clik/parobject.py (from src/python/clik/parobject.py)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/parobject.pyo (from build/src/python/clik/parobject.pyo)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/miniparse.pyc (from build/src/python/clik/miniparse.pyc)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/__init__.pyo (from build/src/python/clik/__init__.pyo)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/miniparse.pyo (from build/src/python/clik/miniparse.pyo)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/src/python/clik/miniparse.py (from src/python/clik/miniparse.py)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/src/python/clik/smicahlp.py (from src/python/clik/smicahlp.py)
- install /home/narayan/Cosmo_Programs/plc-2.0/share/clik/rel2015/ksz_fromcamspec.dat (from src/plik/component_plugin/rel2015/ksz_fromcamspec.dat)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/smicahlp.pyc (from build/src/python/clik/smicahlp.pyc)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/__init__.pyc (from build/src/python/clik/__init__.pyc)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/smicahlp.pyo (from build/src/python/clik/smicahlp.pyo)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/hpy.pyc (from build/src/python/clik/hpy.pyc)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/src/python/clik/hpy.py (from src/python/clik/hpy.py)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/hpy.pyo (from build/src/python/clik/hpy.pyo)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/cldf.pyc (from build/src/python/clik/cldf.pyc)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/src/python/clik/cldf.py (from src/python/clik/cldf.py)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/cldf.pyo (from build/src/python/clik/cldf.pyo)
- install /home/narayan/Cosmo_Programs/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/narayan/Cosmo_Programs/plc-2.0/bin/clik_example_py (from build/src/python/clik_example_py)
+ install /home/narayan/Cosmo_Programs/plc-2.0/bin/clik_change_lrange (from build/src/python/clik_change_lrange)
+ install /home/narayan/Cosmo_Programs/plc-2.0/bin/clik_explore_1d (from build/src/python/clik_explore_1d)
+ install /home/narayan/Cosmo_Programs/plc-2.0/bin/clik_get_selfcheck (from build/src/python/clik_get_selfcheck)
+ install /home/narayan/Cosmo_Programs/plc-2.0/bin/clik_print (from build/src/python/clik_print)
+ install /home/narayan/Cosmo_Programs/plc-2.0/bin/prepare_wmap (from build/src/python/prepare_wmap)
- install /home/narayan/Cosmo_Programs/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)
[ 59/125] Processing src/lowlike/Planck_teeebb_pixlike.F90
- install /home/narayan/Cosmo_Programs/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)
[ 60/125] Processing src/bflike/long_intrinsic_smw.f90
[ 61/125] Processing src/plik/clik_plik.f90
[ 62/125] Compiling src/clik_example_f90.f90
[ 63/125] Processing src/bflike/fitstools_smw.f90
[ 64/125] Processing src/cmbonly/clik_cmbonly.f90
/home/narayan/.local/lib/python2.7/site-packages/Cython-0.29.10-py2.7-linux-x86_64.egg/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/narayan/Cosmo_Programs/plc-2.0/src/plik/component_plugin/rel2015/rel2015.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
+ install /home/narayan/Cosmo_Programs/plc-2.0/lib/python2.7/site-packages/clik/parobject.pyc (from build/src/python/clik/parobject.pyc)
/home/narayan/.local/lib/python2.7/site-packages/Cython-0.29.10-py2.7-linux-x86_64.egg/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/narayan/Cosmo_Programs/plc-2.0/src/python/clik/lkl.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
warning: /home/narayan/Cosmo_Programs/plc-2.0/src/python/clik/lkl.pyx:4:8: 'stdlib' is deprecated, use 'libc.stdlib'
warning: /home/narayan/Cosmo_Programs/plc-2.0/src/python/clik/lkl.pyx:5:8: 'stdio' is deprecated, use 'libc.stdio'
warning: /home/narayan/Cosmo_Programs/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/narayan/Cosmo_Programs/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/narayan/Cosmo_Programs/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/narayan/Cosmo_Programs/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.
/home/narayan/.local/lib/python2.7/site-packages/Cython-0.29.10-py2.7-linux-x86_64.egg/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/narayan/Cosmo_Programs/plc-2.0/src/python/clik/lkl_lensing.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
warning: /home/narayan/Cosmo_Programs/plc-2.0/src/python/clik/lkl_lensing.pyx:4:8: 'stdlib' is deprecated, use 'libc.stdlib'
warning: /home/narayan/Cosmo_Programs/plc-2.0/src/python/clik/lkl_lensing.pyx:5:8: 'stdio' is deprecated, use 'libc.stdio'
warning: /home/narayan/Cosmo_Programs/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/narayan/Cosmo_Programs/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/narayan/Cosmo_Programs/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/narayan/Cosmo_Programs/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.
[ 66/125] Processing src/camspec/clik_CAMspec.F90
[ 67/125] Processing src/bflike/bflike_QUonly.f90
[ 68/125] Processing src/bflike/bflike.f90
[ 69/125] Processing src/bflike/bflike_smw.f90
[ 70/125] Processing src/lowlike/Planck_likelihood.F90
[ 71/125] Processing src/lowlike/clik_lowlike.f90
/home/narayan/.local/lib/python2.7/site-packages/Cython-0.29.10-py2.7-linux-x86_64.egg/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/narayan/Cosmo_Programs/plc-2.0/src/python/clik/clik.parametric.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: /home/narayan/Cosmo_Programs/plc-2.0/src/python/clik/parametric.pyx:4:8: 'stdlib' is deprecated, use 'libc.stdlib'
warning: /home/narayan/Cosmo_Programs/plc-2.0/src/python/clik/parametric.pyx:5:8: 'stdio' is deprecated, use 'libc.stdio'
[ 72/125] Compiling src/plik/component_plugin/rel2015/fg2015.c
[ 73/125] Compiling src/plik/clik_hfipack.c
[ 74/125] Compiling build/src/python/clik/lkl.pyx.c
[ 75/125] Compiling src/plik/component_plugin/rel2015/leakage.c
[ 76/125] Compiling build/src/python/clik/parametric.pyx.c
[ 77/125] Compiling src/bflike/clik_bflike.c
[ 78/125] Compiling src/plik/component_plugin/rel2015/corrnoise.c
[ 79/125] Compiling src/cldf/cfrd.c
[ 80/125] Compiling src/minipmc/io.c
[ 81/125] Compiling src/plik/clik_plik.c
[ 82/125] Compiling src/lklbs.c
[ 83/125] Compiling src/minipmc/distribution.c
[ 84/125] Compiling src/clik_lensing.c
[ 85/125] Compiling src/lenslike/plenslike/plenslike_dat_qecl.c
[ 86/125] Compiling src/clik_fortran.c
[ 87/125] Compiling src/clik_dic.c
[ 88/125] Compiling src/gibbs/clik_gibbs.c
[ 89/125] Compiling src/clik.c
[ 90/125] Compiling src/lowly_common.c
[ 91/125] Compiling src/camspec/clik_CAMspec.c
[ 92/125] Compiling src/plik/clik_parametric_addon.c
src/python/clik/lkl.pyx.c(4618): error: identifier "NPY_ARRAY_C_CONTIGUOUS" is undefined
__pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_ARRAY_C_CONTIGUOUS) != 0)) != 0);
^
src/python/clik/lkl.pyx.c(4674): error: identifier "NPY_ARRAY_F_CONTIGUOUS" is undefined
__pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_ARRAY_F_CONTIGUOUS) != 0)) != 0);
^
compilation aborted for src/python/clik/lkl.pyx.c (code 2)
src/python/clik/parametric.pyx.c(18703): error: identifier "NPY_ARRAY_C_CONTIGUOUS" is undefined
__pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_ARRAY_C_CONTIGUOUS) != 0)) != 0);
^
src/python/clik/parametric.pyx.c(18759): error: identifier "NPY_ARRAY_F_CONTIGUOUS" is undefined
__pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_ARRAY_F_CONTIGUOUS) != 0)) != 0);
^
compilation aborted for src/python/clik/parametric.pyx.c (code 2)
Waf: Leaving directory `/home/narayan/Cosmo_Programs/plc-2.0/build'
Build failed
-> task in 'lkl' failed (exit status 2):
{task 139625554634896: c lkl.pyx.c -> lkl.pyx.c.1.o}
['/home/softwares/intel/compilers_and_libraries_2019.1.144/linux/bin/intel64/icc', '-fopenmp', '-fPIC', '-shared', '-I/home/narayan/Cosmo_Programs/plc-2.0/build/src', '-I/home/narayan/Cosmo_Programs/plc-2.0/src', '-I/home/narayan/Cosmo_Programs/plc-2.0/build/src/minipmc', '-I/home/narayan/Cosmo_Programs/plc-2.0/src/minipmc', '-I/home/softwares/intel/compilers_and_libraries_2019.1.144/linux/mkl/include', '-I/home/narayan/Cosmo_Programs/plc-2.0/include', '-I/usr/include/python2.7', '-I/home/narayan/.local/lib/python2.7/site-packages/numpy/core/include', '-DPYTHONDIR="/usr/lib/python2.7/site-packages"', '-DPYTHONARCHDIR="/usr/lib64/python2.7/site-packages"', '-DHAVE_PYEMBED=1', '-DHAVE_PYTHON_H=1', '-DHAS_LAPACK', '-DHAS_MKL', 'src/python/clik/lkl.pyx.c', '-c', '-o', '/home/narayan/Cosmo_Programs/plc-2.0/build/src/python/clik/lkl.pyx.c.1.o']
-> task in 'parametric' failed (exit status 2):
{task 139625554636112: c parametric.pyx.c -> parametric.pyx.c.3.o}
['/home/softwares/intel/compilers_and_libraries_2019.1.144/linux/bin/intel64/icc', '-fopenmp', '-fPIC', '-shared', '-I/home/narayan/Cosmo_Programs/plc-2.0/build/src', '-I/home/narayan/Cosmo_Programs/plc-2.0/src', '-I/home/narayan/Cosmo_Programs/plc-2.0/build/src/plik', '-I/home/narayan/Cosmo_Programs/plc-2.0/src/plik', '-I/home/narayan/Cosmo_Programs/plc-2.0/build/src/minipmc', '-I/home/narayan/Cosmo_Programs/plc-2.0/src/minipmc', '-I/home/softwares/intel/compilers_and_libraries_2019.1.144/linux/mkl/include', '-I/home/narayan/Cosmo_Programs/plc-2.0/include', '-I/usr/include/python2.7', '-I/home/narayan/.local/lib/python2.7/site-packages/numpy/core/include', '-DPYTHONDIR="/usr/lib/python2.7/site-packages"', '-DPYTHONARCHDIR="/usr/lib64/python2.7/site-packages"', '-DHAVE_PYEMBED=1', '-DHAVE_PYTHON_H=1', '-DHAS_LAPACK', '-DHAS_MKL', 'src/python/clik/parametric.pyx.c', '-c', '-o', '/home/narayan/Cosmo_Programs/plc-2.0/build/src/python/clik/parametric.pyx.c.3.o']
CosmoMC itself is running fine without plc-2.0.
Maybe I missed something. Please help. Thank you in advance.
Regards
Srijita