rsnemmen / chombo

Chombo 3.2, including support for Pluto

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Astrophysicist. Data scientist. Professor. Research Scientist. Team Leader. Curious person.

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chombo's Issues

make lib error

make lib gives the following error

make --no-print-directory --directory=/home/alankar/Documents/Pluto/pluto-4.2/PLUTO/Lib/Chombo-3.2/lib/src/AMRElliptic  lib
/bin/sh: 1: test: -ge: unexpected operator
/bin/sh: 1: test: -ge: unexpected operator
/bin/sh: 1: test: -ge: unexpected operator
Depending MACProjectorF.ChF ...
Depending NewPoissonOp4F.ChF ...
Depending VCAMRPoissonOpF.ChF ...
Depending CCProjectorF.ChF ...
Depending AMRNodeOpF.ChF ...
Depending ResistivityOpF.ChF ...
Depending LevelTGAF.ChF ...
Depending ViscousTensorOpF.ChF ...
Depending AMRPoissonOpF.ChF ...
Depending LevelTGA.cpp ...
Depending PetscCompGridPois.cpp ...
Depending NewPoissonOp4.cpp ...
Depending PetscCompGrid.cpp ...
Depending AMRNodeOp.cpp ...
Depending PetscSolver.cpp ...
Depending ResistivityOp.cpp ...
Depending BCFunc.cpp ...
Depending NodeQCFI.cpp ...
Depending NodeBCFunc.cpp ...
Depending NodeLevelDataOps.cpp ...
Depending ViscousTensorOp.cpp ...
Depending PetscCompGridVTO.cpp ...
Depending NewPoissonOp.cpp ...
Depending VCAMRPoissonOp2.cpp ...
Depending AMRPoissonOp.cpp ...
Depending BackwardEuler.cpp ...
/bin/sh: 1: test: -ge: unexpected operator
/bin/sh: 1: test: -ge: unexpected operator
/bin/sh: 1: test: -ge: unexpected operator
mpic++  -O2 -funroll-loops -Wno-unknown-pragmas -Wno-long-long -Wno-sign-compare -Wno-deprecated -ftemplate-depth-25  -Wno-variadic-macros -m64    -DCH_SPACEDIM=3 -DCH_Linux    -DCH_MPI -DMPICH_SKIP_MPICXX -ULAM_WANT_MPI2CPP -DMPI_NO_CPPBIND    -DCH_USE_SETVAL -DCH_USE_COMPLEX   -DCH_USE_MEMORY_TRACKING  -DCH_USE_64 -DCH_USE_DOUBLE -DCH_USE_HDF5 -I/home/alankar/comp_bin/include -DH5_USE_16_API        -DCH_FORT_UNDERSCORE -I/home/alankar/Documents/Pluto/pluto-4.2/PLUTO/Lib/Chombo-3.2/lib/src/AMRElliptic/../../src/AMRTools -I/home/alankar/Documents/Pluto/pluto-4.2/PLUTO/Lib/Chombo-3.2/lib/src/AMRElliptic/../../src/BoxTools -I/home/alankar/Documents/Pluto/pluto-4.2/PLUTO/Lib/Chombo-3.2/lib/src/AMRElliptic/../../src/BaseTools    -DCH_LANG_CC -c BackwardEuler.cpp -o o/3d.Linux.64.mpic++.gfortran.OPT.MPI.O3/BackwardEuler.o
In file included from /usr/include/c++/7/bits/move.h:54:0,
                 from /usr/include/c++/7/bits/nested_exception.h:40,
                 from /usr/include/c++/7/exception:143,
                 from /usr/include/c++/7/ios:39,
                 from /usr/include/c++/7/ostream:38,
                 from /usr/include/c++/7/iostream:39,
                 from BackwardEuler.cpp:14:
/usr/include/c++/7/type_traits: In instantiation of ‘struct std::__or_<std::is_lvalue_reference<std::locale&>, std::is_rvalue_reference<std::locale&> >’:
/usr/include/c++/7/type_traits:580:12:   required from ‘struct std::is_reference<std::locale&>’
/usr/include/c++/7/type_traits:120:12:   required from ‘struct std::__or_<std::is_reference<std::locale&>, std::is_void<std::locale&> >’
/usr/include/c++/7/type_traits:125:12:   required from ‘struct std::__or_<std::is_function<std::locale&>, std::is_reference<std::locale&>, std::is_void<std::locale&> >’
/usr/include/c++/7/type_traits:154:31:   required from ‘struct std::__not_<std::__or_<std::is_function<std::locale&>, std::is_reference<std::locale&>, std::is_void<std::locale&> > >’
/usr/include/c++/7/type_traits:600:12:   required from ‘struct std::is_object<std::locale&>’
/usr/include/c++/7/type_traits:120:12:   [ skipping 14 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/c++/7/type_traits:1159:12:   required from ‘struct std::__is_move_constructible_impl<std::locale, true>’
/usr/include/c++/7/type_traits:1165:12:   required from ‘struct std::is_move_constructible<std::locale>’
/usr/include/c++/7/type_traits:143:12:   required from ‘struct std::__and_<std::is_move_constructible<std::locale>, std::is_move_assignable<std::locale> >’
/usr/include/c++/7/type_traits:148:12:   required from ‘struct std::__and_<std::__not_<std::__is_tuple_like<std::locale> >, std::is_move_constructible<std::locale>, std::is_move_assignable<std::locale> >’
/usr/include/c++/7/bits/move.h:187:5:   required by substitution of ‘template<class _Tp> typename std::enable_if<std::__and_<std::__not_<std::__is_tuple_like<_Tp> >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> >::value>::type std::swap(_Tp&, _Tp&) [with _Tp = std::locale]’
/usr/include/c++/7/streambuf:819:45:   required from here
/usr/include/c++/7/type_traits:120:12: fatal error: template instantiation depth exceeds maximum of 25 (use -ftemplate-depth= to increase the maximum)
     struct __or_<_B1, _B2>
            ^~~~~~~~~~~~~~~
compilation terminated.
/home/alankar/Documents/Pluto/pluto-4.2/PLUTO/Lib/Chombo-3.2/lib/src/AMRElliptic/../../mk/Make.rules:460: recipe for target 'o/3d.Linux.64.mpic++.gfortran.OPT.MPI.O3/BackwardEuler.o' failed
make[1]: *** [o/3d.Linux.64.mpic++.gfortran.OPT.MPI.O3/BackwardEuler.o] Error 1
GNUmakefile:443: recipe for target 'AMRElliptic' failed
make: *** [AMRElliptic] Error 2

Following is the Make.defs.local file I used

# Copy this file to:
#
#    Chombo/lib/mk/Make.defs.local
#
# before modifying it.
#
# Use this file to set Chombo makefile variables for the local
# installation.  To set variables for just a single computer
# create a file named:
#
#    Chombo/lib/mk/local/Make.defs.<hostname>
#
# where <hostname> is the value of `uname -n` (or `hostname`, if uname doesn't work)

# The default values for the main variables here are in:
#
#    Chombo/lib/mk/Make.defs.defaults

# This file is include'd from Make.defs after:
#    Make.defs.defaults
# and before:
#    Make.defs.<hostname> Make.defs.config Make.rules

makefiles+=Make.defs.local

################################################################

# Chombo configuration variables that affect filenames:

#  DIM          :(2,3) number of dimensions in PDEs
#  DEBUG        :(TRUE,FALSE) compile with symbol table or not
#  OPT          :(TRUE,HIGH,FALSE) optimize, high optimize, or not
#  PRECISION    :(FLOAT,DOUBLE) size of floating point variables
#  PROFILE      :(TRUE,FALSE) compile for performance profiling or not
#  CXX          : command to compile/link C++ code
#  FC           : command to compile Fortran code
#  MPI          :(TRUE,FALSE) compile for parallel if TRUE, else serial
#  OPENMPCC     : TRUE for threading with OpenMP, FALSE without OpenMP
#  MPICXX       : command to compile/link C++ code in parallel
#  OBJMODEL     : special config for non-default compiler mode
#  XTRACONFIG   : user-defined special config

# Variables for optional features that don't affect filenames:

#  USE_64          : if TRUE, use 64bit pointers on systems where 32bits is the default
#  USE_COMPLEX     : if TRUE, enable the 'Complex' type
#                    (default is TRUE, disable only if compiler doesn't allow it)
#  USE_EB          : if TRUE, build Chombo Embedded Boundary code
#  USE_CCSE        : if TRUE, build CCSE mglib and supporting code into one lib
#  USE_HDF         : if TRUE, use the HDF5 library
#   HDFINCFLAGS    : cpp options (-I*) for HDF5 include files
#   HDFLIBFLAGS    : link options (-L* -l*) for HDF5 library files
#   HDFMPIINCFLAGS : cpp options (-I*) for parallel HDF5 include files
#   HDFMPILIBFLAGS : link options (-L* -l*) for parallel HDF5 library files
#  USE_MF          : if TRUE, build Chombo MultiFluid code (requires USE_EB=TRUE)
#  USE_MT          : if TRUE, enable Chombo memory tracking
#  USE_SETVAL      : (TRUE,FALSE) use setVal to initialize all BaseFab<Real>

# These variables are system-dependent but usually dont have to be changed:

#  CH_AR       : command to add object files to a library file
#  CH_CPP      : command to run the C preprocessor on Fortran files
#  DOXYGEN  : command to run the 'doyxgen' program
#  LD       : command to run the linker (default: use $CXX or $MPICXX, as appropriate)
#  PERL     : command to run perl
#  RANLIB   : command to post-process a library archive for random access

# Compiler variables.  The 'Make.rules' file chooses whether to use
# the 'opt' flags or the 'dbg' flags.  The 'prof' flags are added if
# PROFILE=TRUE.
#
#  cppdbgflags : debug options for the C-preprocessor (both C++ and Fortran)
#  cppoptflags : optimization options for the C-preprocessor (")
#  cxxcppflags : C-preprocessor flags for C++ compiles only
#  cxxdbgflags : debug options for the C++ and MPIC++ compilers
#  cxxoptflags : optimization options for the C++ and MPIC++ compilers
#  cxxprofflags: profiling options for the C++ and MPIC++ compilers
#  fcppflags   : C-preprocessor flags for Fortran compiles only
#  fdbgflags   : debug options for the Fortran compiler
#  foptflags   : optimization options for the Fortran compiler
#  fprofflags  : profiling options for the Fortran compiler
#  lddbgflags  : debug options for the linker
#  ldoptflags  : optimization options for the linker
#  ldprofflags : profiling options for the linker
#  flibflags   : options for the linker to specify the Fortran libraries
#                (this usually is needed only when mixing C++ and
#                 Fortran compilers from different vendors)
#  syslibflags : extra linker options to get libraries needed on this system
#
# Notes:
# 1) The linker command always uses the CXX options in addition to its own variables,
#    so options that are common to both do not need to be repeated in the ld*flags vars
#    (e.g. -g for debugging, or -pg for profiling)
# 2) The compiler options can be set on the command line using the
#    variables: CPPFLAGS CXXFLAGS FFLAGS LDFLAGS.
#    These variables supercede any settings in the makefiles.
# 3) The GNUmakefile in "Chombo/lib" will check these variables and complain if
#    they have invalid values.  On systems that don't have MPI installed, the
#    various MPI variables should not be set (or should be set to empty strings)
#    to prevent the checker from complaining.

#begin  -- dont change this line

## Override the default values here

## Configuration variables
## Configuration variables
DIM = 3
DEBUG = FALSE
OPT = TRUE
PRECISION = DOUBLE
PROFILE = FALSE
CXX = g++
FC = gfortran
MPI = TRUE
## Note: don’t set the MPICXX variable if you don’t have MPI installed
MPICXX = mpic++
CXXFLAGS=-O3 
FFLAGS=-O3
#OBJMODEL =
XTRACONFIG = .O3
## Optional features
USE_64 = TRUE
#USE_COMPLEX =
#USE_EB =
#USE_CCSE =
USE_HDF = TRUE
HDFINCFLAGS = -I/home/alankar/comp_bin/hdfserial/include 
HDFLIBFLAGS = -L/home/alankar/comp_bin/hdfserial/lib -lhdf5 -lz
## Note: don’t set the HDFMPI* variables if you don’t have parallel HDF installed
HDFMPIINCFLAGS= -I/home/alankar/comp_bin/include -DH5_USE_16_API
HDFMPILIBFLAGS= -L/home/alankar/comp_bin/lib -lhdf5 -lz
#USE_MF        =
#USE_MT        =
#USE_SETVAL    =
#CH_AR         =
#CH_CPP        =
DOXYGEN        = /usr/bin/doxygen
#LD            =
PERL           = /usr/bin/perl
#RANLIB        =
#cppdbgflags   =
#cppoptflags   =
#cxxcppflags   =
#cxxdbgflags   =
#cxxoptflags   =
#cxxprofflags  =
#fcppflags     =
#fdbgflags     =
#foptflags     =
#fprofflags    =
#flibflags     =
#lddbgflags    =
#ldoptflags    =
#ldprofflags   =
#syslibflags   =

#end  -- dont change this line