Problem compiling Cantera on Arch Linux!
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Eduardo W.
Apr 2, 2018, 2:39:51 PM4/2/18
to Cantera Users' Group
Greetings!
I am trying to compile Cantera from source (git clone'd it), but I'm stumbling upon problems with sundial. I'm running Manjaro (which is, actually, Arch) with the kernel 4.14.27-1-MANJARO, gcc 7.3.1 and python 3.6.4 Anaconda. I know I could install it through conda, but I want the C++ libraries.
When I try to build, I receive the log below. It looks like building was going well until it tried to compile something that used sundial. I installed the most recent sundial package from the AUR repository. Anyone can give me some help with this?
I am trying to compile Cantera from source (git clone'd it), but I'm stumbling upon problems with sundial. I'm running Manjaro (which is, actually, Arch) with the kernel 4.14.27-1-MANJARO, gcc 7.3.1 and python 3.6.4 Anaconda. I know I could install it through conda, but I want the C++ libraries.
When I try to build, I receive the log below. It looks like building was going well until it tried to compile something that used sundial. I installed the most recent sundial package from the AUR repository. Anyone can give me some help with this?
scons: Reading SConscript files ...
INFO: SCons is using the following Python interpreter: /usr/bin/python2
Configuration variables read from 'cantera.conf' and command line:
Checking for C++ header file cmath... (cached) yes
Checking for C++ header file fmt/ostream.h... (cached) no
INFO: Using private installation of fmt library.
Checking for C++ header file gtest/gtest.h... (cached) no
Checking for C++ header file Eigen/Dense... (cached) no
Checking whether __GLIBCXX__ is declared... (cached) yes
Checking whether _LIBCPP_VERSION is declared... (cached) no
INFO: Found Boost version '1_66'
Checking for CVodeCreate(CV_BDF, CV_NEWTON) in C++ library sundials_cvodes... (cached) no
Checking for double x; log(x) in C library None... (cached) no
INFO: Using private installation of Sundials version 2.6.
INFO: Using 'gfortran' to build the Fortran 90 interface
INFO: Using Cython version 0.28.1.
WARNING: Not building the full Python 2 package because the Python 2 interpreter '/usr/bin/python2' could not be found or a required dependency (e.g. numpy) was not found.
NumPy for Python 2.7 not found.
INFO: Using NumPy version 1.14.0 for Python 3.6.
INFO: Building Python package for Python 3.6
scons: done reading SConscript files.
scons: Building targets ...
ConfigBuilder(["include/cantera/ext/sundials/sundials_config.h"], ["ext/sundials_config.h.in"])
Generating include/cantera/ext/sundials/sundials_config.h with the following settings:
SUNDIALS_USE_GENERIC_MATH 1
SUNDIALS_BLAS_LAPACK *undefined*
ConfigBuilder(["build/src/config.h.build"], ["include/cantera/base/config.h.in"])
Generating build/src/config.h.build with the following settings:
CANTERA_SHORT_VERSION "2.3"
CANTERA_VERSION "2.3.0"
FTN_TRAILING_UNDERSCORE 1
LAPACK_FTN_STRING_LEN_AT_END 1
LAPACK_FTN_TRAILING_UNDERSCORE 1
LAPACK_NAMES_LOWERCASE 1
SUNDIALS_USE_LAPACK 0
SUNDIALS_VERSION 26
gfortran -o build/src/fortran/fctxml_interface.o -c -O3 -Ibuild/src/fortran -Isrc/fortran -Isrc/fortran -Jbuild/src/fortran src/fortran/fctxml_interface.f90
gfortran -o build/src/fortran/cantera_xml.o -c -O3 -Ibuild/src/fortran -Isrc/fortran -Isrc/fortran -Jbuild/src/fortran src/fortran/cantera_xml.f90
gfortran -o build/src/fortran/fct_interface.o -c -O3 -Ibuild/src/fortran -Isrc/fortran -Isrc/fortran -Jbuild/src/fortran src/fortran/fct_interface.f90
gfortran -o build/src/fortran/cantera_thermo.o -c -O3 -Ibuild/src/fortran -Isrc/fortran -Isrc/fortran -Jbuild/src/fortran src/fortran/cantera_thermo.f90
gfortran -o build/src/fortran/cantera_kinetics.o -c -O3 -Ibuild/src/fortran -Isrc/fortran -Isrc/fortran -Jbuild/src/fortran src/fortran/cantera_kinetics.f90
gfortran -o build/src/fortran/cantera_iface.o -c -O3 -Ibuild/src/fortran -Isrc/fortran -Isrc/fortran -Jbuild/src/fortran src/fortran/cantera_iface.f90
gfortran -o build/src/fortran/cantera_transport.o -c -O3 -Ibuild/src/fortran -Isrc/fortran -Isrc/fortran -Jbuild/src/fortran src/fortran/cantera_transport.f90
gfortran -o build/src/fortran/cantera_funcs.o -c -O3 -Ibuild/src/fortran -Isrc/fortran -Isrc/fortran -Jbuild/src/fortran src/fortran/cantera_funcs.f90
gfortran -o build/src/fortran/cantera.o -c -O3 -Ibuild/src/fortran -Isrc/fortran -Isrc/fortran -Jbuild/src/fortran src/fortran/cantera.f90
g++ -o build/src/fortran/fct.o -c -std=c++0x -pthread -O3 -Wno-inline -g -DNDEBUG -Iinclude -Isrc src/fortran/fct.cpp
g++ -o build/src/fortran/fctxml.o -c -std=c++0x -pthread -O3 -Wno-inline -g -DNDEBUG -Iinclude -Isrc src/fortran/fctxml.cpp
ar rc build/lib/libcantera_fortran.a build/src/fortran/cantera.o build/src/fortran/cantera_funcs.o build/src/fortran/cantera_iface.o build/src/fortran/cantera_kinetics.o build/src/fortran/cantera_thermo.o build/src/fortran/cantera_transport.o build/src/fortran/cantera_xml.o build/src/fortran/fct_interface.o build/src/fortran/fctxml_interface.o build/src/fortran/fct.o build/src/fortran/fctxml.o
ranlib build/lib/libcantera_fortran.a
gcc -o build/ext/sundials/src/sundials/sundials_band.os -c -pthread -O3 -Wno-inline -g -w -fPIC -DNDEBUG -Iinclude/cantera/ext ext/sundials/src/sundials/sundials_band.c
In file included from include/cantera/ext/sundials/sundials_band.h:32:0,
from ext/sundials/src/sundials/sundials_band.c:26:
include/cantera/ext/sundials/sundials_direct.h:116:3: error: unknown type name 'sunindextype'
sunindextype M;
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:117:3: error: unknown type name 'sunindextype'
sunindextype N;
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:118:3: error: unknown type name 'sunindextype'
sunindextype ldim;
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:119:3: error: unknown type name 'sunindextype'
sunindextype mu;
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:120:3: error: unknown type name 'sunindextype'
sunindextype ml;
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:121:3: error: unknown type name 'sunindextype'
sunindextype s_mu;
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:123:3: error: unknown type name 'sunindextype'
sunindextype ldata;
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:197:36: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT DlsMat NewDenseMat(sunindextype M, sunindextype N);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:197:52: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT DlsMat NewDenseMat(sunindextype M, sunindextype N);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:219:35: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT DlsMat NewBandMat(sunindextype N, sunindextype mu, sunindextype ml, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:219:51: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT DlsMat NewBandMat(sunindextype N, sunindextype mu, sunindextype ml, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:219:68: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT DlsMat NewBandMat(sunindextype N, sunindextype mu, sunindextype ml, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:219:85: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT DlsMat NewBandMat(sunindextype N, sunindextype mu, sunindextype ml, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:253:17: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT sunindextype *NewIndexArray(sunindextype N);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:253:45: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT sunindextype *NewIndexArray(sunindextype N);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:265:40: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT realtype *NewRealArray(sunindextype N);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:323:40: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT realtype **newDenseMat(sunindextype m, sunindextype n);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:323:56: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT realtype **newDenseMat(sunindextype m, sunindextype n);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:324:39: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT realtype **newBandMat(sunindextype n, sunindextype smu, sunindextype ml);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:324:55: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT realtype **newBandMat(sunindextype n, sunindextype smu, sunindextype ml);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:324:73: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT realtype **newBandMat(sunindextype n, sunindextype smu, sunindextype ml);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:327:17: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT sunindextype *newIndexArray(sunindextype n);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:327:45: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT sunindextype *newIndexArray(sunindextype n);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_direct.h:328:40: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT realtype *newRealArray(sunindextype m);
^~~~~~~~~~~~
In file included from ext/sundials/src/sundials/sundials_band.c:26:0:
include/cantera/ext/sundials/sundials_band.h:84:17: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT sunindextype BandGBTRF(DlsMat A, sunindextype *p);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:84:50: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT sunindextype BandGBTRF(DlsMat A, sunindextype *p);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:85:17: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT sunindextype bandGBTRF(realtype **a, sunindextype n, sunindextype mu, sunindextype ml,
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:85:54: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT sunindextype bandGBTRF(realtype **a, sunindextype n, sunindextype mu, sunindextype ml,
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:85:70: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT sunindextype bandGBTRF(realtype **a, sunindextype n, sunindextype mu, sunindextype ml,
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:85:87: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT sunindextype bandGBTRF(realtype **a, sunindextype n, sunindextype mu, sunindextype ml,
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:86:36: error: unknown type name 'sunindextype'
sunindextype smu, sunindextype *p);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:86:54: error: unknown type name 'sunindextype'
sunindextype smu, sunindextype *p);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:105:42: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void BandGBTRS(DlsMat A, sunindextype *p, realtype *b);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:106:46: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void bandGBTRS(realtype **a, sunindextype n, sunindextype smu,
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:106:62: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void bandGBTRS(realtype **a, sunindextype n, sunindextype smu,
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:107:32: error: unknown type name 'sunindextype'
sunindextype ml, sunindextype *p, realtype *b);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:107:49: error: unknown type name 'sunindextype'
sunindextype ml, sunindextype *p, realtype *b);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:124:51: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void BandCopy(DlsMat A, DlsMat B, sunindextype copymu, sunindextype copyml);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:124:72: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void BandCopy(DlsMat A, DlsMat B, sunindextype copymu, sunindextype copyml);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:125:59: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void bandCopy(realtype **a, realtype **b, sunindextype n,
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:126:31: error: unknown type name 'sunindextype'
sunindextype a_smu, sunindextype b_smu,
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:126:51: error: unknown type name 'sunindextype'
sunindextype a_smu, sunindextype b_smu,
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:127:10: error: unknown type name 'sunindextype'
sunindextype copymu, sunindextype copyml);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:127:31: error: unknown type name 'sunindextype'
sunindextype copymu, sunindextype copyml);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:144:58: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void bandScale(realtype c, realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:144:74: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void bandScale(realtype c, realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:144:91: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void bandScale(realtype c, realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:144:108: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void bandScale(realtype c, realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:155:52: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void bandAddIdentity(realtype **a, sunindextype n, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:155:68: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void bandAddIdentity(realtype **a, sunindextype n, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:173:73: error: unknown type name 'sunindextype'
SUNDIALS_EXPORT void bandMatvec(realtype **a, realtype *x, realtype *y, sunindextype n,
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:174:3: error: unknown type name 'sunindextype'
sunindextype mu, sunindextype ml, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:174:20: error: unknown type name 'sunindextype'
sunindextype mu, sunindextype ml, sunindextype smu);
^~~~~~~~~~~~
include/cantera/ext/sundials/sundials_band.h:174:37: error: unknown type name 'sunindextype'
sunindextype mu, sunindextype ml, sunindextype smu);
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:40:1: error: unknown type name 'sunindextype'
sunindextype BandGBTRF(DlsMat A, sunindextype *p)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:40:34: error: unknown type name 'sunindextype'
sunindextype BandGBTRF(DlsMat A, sunindextype *p)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:45:26: error: unknown type name 'sunindextype'
void BandGBTRS(DlsMat A, sunindextype *p, realtype *b)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:50:35: error: unknown type name 'sunindextype'
void BandCopy(DlsMat A, DlsMat B, sunindextype copymu, sunindextype copyml)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:50:56: error: unknown type name 'sunindextype'
void BandCopy(DlsMat A, DlsMat B, sunindextype copymu, sunindextype copyml)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:71:1: error: unknown type name 'sunindextype'
sunindextype bandGBTRF(realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu, sunindextype *p)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:71:38: error: unknown type name 'sunindextype'
sunindextype bandGBTRF(realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu, sunindextype *p)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:71:54: error: unknown type name 'sunindextype'
sunindextype bandGBTRF(realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu, sunindextype *p)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:71:71: error: unknown type name 'sunindextype'
sunindextype bandGBTRF(realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu, sunindextype *p)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:71:88: error: unknown type name 'sunindextype'
sunindextype bandGBTRF(realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu, sunindextype *p)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:71:106: error: unknown type name 'sunindextype'
sunindextype bandGBTRF(realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu, sunindextype *p)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:177:30: error: unknown type name 'sunindextype'
void bandGBTRS(realtype **a, sunindextype n, sunindextype smu, sunindextype ml, sunindextype *p, realtype *b)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:177:46: error: unknown type name 'sunindextype'
void bandGBTRS(realtype **a, sunindextype n, sunindextype smu, sunindextype ml, sunindextype *p, realtype *b)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:177:64: error: unknown type name 'sunindextype'
void bandGBTRS(realtype **a, sunindextype n, sunindextype smu, sunindextype ml, sunindextype *p, realtype *b)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:177:81: error: unknown type name 'sunindextype'
void bandGBTRS(realtype **a, sunindextype n, sunindextype smu, sunindextype ml, sunindextype *p, realtype *b)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:209:43: error: unknown type name 'sunindextype'
void bandCopy(realtype **a, realtype **b, sunindextype n, sunindextype a_smu, sunindextype b_smu,
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:209:59: error: unknown type name 'sunindextype'
void bandCopy(realtype **a, realtype **b, sunindextype n, sunindextype a_smu, sunindextype b_smu,
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:209:79: error: unknown type name 'sunindextype'
void bandCopy(realtype **a, realtype **b, sunindextype n, sunindextype a_smu, sunindextype b_smu,
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:210:15: error: unknown type name 'sunindextype'
sunindextype copymu, sunindextype copyml)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:210:36: error: unknown type name 'sunindextype'
sunindextype copymu, sunindextype copyml)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:225:42: error: unknown type name 'sunindextype'
void bandScale(realtype c, realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:225:58: error: unknown type name 'sunindextype'
void bandScale(realtype c, realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:225:75: error: unknown type name 'sunindextype'
void bandScale(realtype c, realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:225:92: error: unknown type name 'sunindextype'
void bandScale(realtype c, realtype **a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:239:36: error: unknown type name 'sunindextype'
void bandAddIdentity(realtype **a, sunindextype n, sunindextype smu)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:239:52: error: unknown type name 'sunindextype'
void bandAddIdentity(realtype **a, sunindextype n, sunindextype smu)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:247:57: error: unknown type name 'sunindextype'
void bandMatvec(realtype **a, realtype *x, realtype *y, sunindextype n,
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:248:3: error: unknown type name 'sunindextype'
sunindextype mu, sunindextype ml, sunindextype smu)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:248:20: error: unknown type name 'sunindextype'
sunindextype mu, sunindextype ml, sunindextype smu)
^~~~~~~~~~~~
ext/sundials/src/sundials/sundials_band.c:248:37: error: unknown type name 'sunindextype'
sunindextype mu, sunindextype ml, sunindextype smu)
^~~~~~~~~~~~
scons: *** [build/ext/sundials/src/sundials/sundials_band.os] Error 1
scons: building terminated because of errors.
scons: *** Found dependency cycle(s):
include/cantera/ext/cvodes/cvodes_bbdpre.h -> include/cantera/ext/cvodes/cvodes_bbdpre.h
include/cantera/ext/cvodes/cvodes_bandpre.h -> include/cantera/ext/cvodes/cvodes_bandpre.h
File "/usr/lib/python2.7/site-packages/SCons/Taskmaster.py", line 1065, in cleanup
Chris Neal
Apr 2, 2018, 3:29:53 PM4/2/18
to Cantera Users' Group
It looks like whatever sundials version Cantera is using is not version 3.1. In version 3.1 of Sundials they introduced the "sunindextype" parameter. It's odd because the AUR repository seems to have the newest version of Sundials available. https://aur.archlinux.org/packages/sundials/
This line from the compilation output seems to verify what I have observed: INFO: Using private installation of Sundials version 2.6.
I'm unsure what a 'Private installation" of Sundials is. Does that mean Cantera's version, or a version found on the system. We need to know that.
I'm unsure what a 'Private installation" of Sundials is. Does that mean Cantera's version, or a version found on the system. We need to know that.
Bryan W. Weber
Apr 2, 2018, 3:47:37 PM4/2/18
to Cantera Users' Group
Eduardo,
Did you update the submodules when you cloned/pulled?
git submodule update --init --recursive
should take care of updating Sundials to the most recent version (and the other dependencies as well).
As Chris noted, the compilation is using the version of Sundials 2.6 that used to be included with Cantera.
Best,
Bryan
Ray Speth
Apr 2, 2018, 3:59:16 PM4/2/18
to Cantera Users' Group
Hi All,
Actually, I think what is happening is the opposite. Cantera 2.3.0 expects it’s “private” copy of Sundials (downloaded as a git submodule) to be Sundials 2.6. However, when you just run the git clone --recursive https://github.com/Cantera/cantera.git command, you will get the most recent version of the Sundials mirror repository, which contains Sundials 3.1.0. After checking out the v2.3.0 tag (or the 2.3 branch), you need to check out the correct version of Sundials by running the command git submodule update (which will give an error related to the Eigen submodule, but I think you can ignore this).
Alternatively, try running scons with the option system_sundials=y and work out why that’s failing by checking the config.log file.
Regards,
Ray
Eduardo W.
Apr 3, 2018, 8:50:13 AM4/3/18
to Cantera Users' Group
I hadn't tried this, but it didn't worked:
remote: Counting objects: 157, done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 157 (delta 127), reused 131 (delta 127), pack-reused 26
Receiving objects: 100% (157/157), 69.27 KiB | 375.00 KiB/s, done.
Resolving deltas: 100% (128/128), completed with 116 local objects.
From https://github.com/eigenteam/eigen-git-mirror
0258fe9fc..bf26e658b branches/3.3 -> origin/branches/3.3
c3327783a..852f0704d branches/default -> origin/branches/default
c3327783a..852f0704d master -> origin/master
error: Server does not allow request for unadvertised object c6ef117db0a5d72ad0b0239ab1f6dfc3291c398e
Fetched in submodule path 'ext/eigen', but it did not contain c6ef117db0a5d72ad0b0239ab1f6dfc3291c398e. Direct fetching of that commit failed.
Eduardo W.
Apr 3, 2018, 8:50:19 AM4/3/18
to Cantera Users' Group
I believe this is the way to the root of the problem. Running git submodule update did returned an error in the eigen submodule, which I ignored. When I then tried to build with system_sundials=y it returned and error and asked me to check the log.
scons: Reading SConscript files ...
INFO: SCons is using the following Python interpreter: /usr/bin/python2
Configuration variables read from 'cantera.conf' and command line:
system_sundials = 'y'
Checking for C++ header file cmath... (cached) yes
Checking for C++ header file fmt/ostream.h... (cached) no
INFO: Using private installation of fmt library.
Checking for C++ header file gtest/gtest.h... (cached) no
Checking for C++ header file Eigen/Dense... (cached) no
Checking whether __GLIBCXX__ is declared... (cached) yes
Checking whether _LIBCPP_VERSION is declared... (cached) no
INFO: Found Boost version '1_66'
Checking for CVodeCreate(CV_BDF, CV_NEWTON) in C++ library sundials_cvodes... (cached) no
ERROR: Expected system installation of Sundials, but it could not be found.
See 'config.log' for details.
I cleaned the build with scons clean and deleted the old log because scons just appends more information to it, so I could see a clean build log after building it from scratch again. The relevant lines are pasted below. Strange, it seems it can't find my local installation of the sundials package...
scons: Configure: Checking for CVodeCreate(CV_BDF, CV_NEWTON) in C++ library sundials_cvodes...
scons: Configure: ".sconf_temp/conftest_7.cpp" is up to date.
scons: Configure: The original builder output was:
|.sconf_temp/conftest_7.cpp <-
| |
| |
| |#include "cvodes/cvodes.h"
| |int
| |main() {
| | CVodeCreate(CV_BDF, CV_NEWTON);
| |return 0;
| |}
| |
|
scons: Configure: Building ".sconf_temp/conftest_7.o" failed in a previous run and all its sources are up to date.
scons: Configure: The original builder output was:
|g++ -o .sconf_temp/conftest_7.o -c -std=c++0x -pthread -O3 -Wno-inline -g -DNDEBUG .sconf_temp/conftest_7.cpp
|
scons: Configure: (cached) noEduardo W.
Apr 3, 2018, 8:51:53 AM4/3/18
to Cantera Users' Group
You know what's strange? I solved it in the most Microsoft way possible: I git clone'd Cantera back again, removed the sundials package I had installed from AUR and gave scons build a go. It compiled and installed flawlessly.
This is way too weird. The only possibility I can imagine was if my package manager was, somehow, locked, because it showed my 92 updates (the only pain in using Arch...). Before I ran pacman -Suy to update everything, I couldn't install anything. Maybe (and this is a big stretch), this could be the cause.
Anyway, thank you all for your time!
This is way too weird. The only possibility I can imagine was if my package manager was, somehow, locked, because it showed my 92 updates (the only pain in using Arch...). Before I ran pacman -Suy to update everything, I couldn't install anything. Maybe (and this is a big stretch), this could be the cause.
Anyway, thank you all for your time!
Davide De Filippo
Jul 2, 2018, 10:51:03 AM7/2/18
to Cantera Users' Group
Hi Eduardo! I had the same problem. could you please explain better how did you solve? I am not an expert but i am trying to install the matlab toolbox :(
Eduardo W.
Jul 2, 2018, 12:23:37 PM7/2/18
to Cantera Users' Group
Hi Davide!
Before I tried my first install, I installed some packages from the AUR to aid on the installation. Among them, Sundials was giving me a headache, and it was the reason I couldn't install it. I then removed the Sundials I had installed from AUR, removed the directory and cloned back the repository to start fresh. Then, I just compiled as instructed, without a prior installation of the Sundials package, and it went flawlessly.
Another possibility was what I discussed. I had a notification of 92 updates. Arch is a bit fiddly with available packages (my computer, for example, won't mount USB devices if I don't restart after updates), so I tried to update my system beforehand.
Try to do the same: Update your system and try again.
I didn't wanted the matlab toolbox, so I went with the vanilla installation, and didn't bothered in checking whether the matlab toolbox was or wasn't installed...
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