jayjaybillings / fern Goto Github PK

Deal intelligently with using compiler flags. Good ones to have are -O and -g. Another one of my favorites is -Wall. We should have a way to deal with flags well.

I'm trying to make FERN after using cmake, but I'm getting this error. I've bolded what is of concern in this issue. Jay suggests that it is due to std::abs() expecting integers when they are being passed doubles. Any thoughts on how to resolve this?

[ 5%] Building CXX object src/CMakeFiles/fern.dir/Globals.cpp.o
[ 10%] Building CXX object src/CMakeFiles/fern.dir/IntegrationData.cpp.o
[ 15%] Building CXX object src/CMakeFiles/fern.dir/JavaComparisonTest.cpp.o
In file included from /Users/Dan/Desktop/Research/FERN/fernRefactor/fern/src/JavaComparisonTest.cpp:40:
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/tpls/fire/parsers/BasicDelimitedTextParser.h:146:26: warning: logical not is only applied to the left hand side of this comparison
[-Wlogical-not-parentheses]
if (!line.empty() && !line.find("#") == 0) {
^ ~~
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/tpls/fire/parsers/BasicDelimitedTextParser.h:146:26: note: add parentheses after the '!' to evaluate the comparison first
if (!line.empty() && !line.find("#") == 0) {
^
( )
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/tpls/fire/parsers/BasicDelimitedTextParser.h:146:26: note: add parentheses around left hand side expression to silence this warning
if (!line.empty() && !line.find("#") == 0) {
^
( )
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/tpls/fire/parsers/BasicDelimitedTextParser.h:146:26: warning: logical not is only applied to the left hand side of this comparison
[-Wlogical-not-parentheses]
if (!line.empty() && !line.find("#") == 0) {
^ ~~
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/src/JavaComparisonTest.cpp:130:9: note: in instantiation of member function 'fire::BasicDelimitedTextParser::parse' requested here
parser.parse();
^
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/tpls/fire/parsers/BasicDelimitedTextParser.h:146:26: note: add parentheses after the '!' to evaluate the comparison first
if (!line.empty() && !line.find("#") == 0) {
^
( )
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/tpls/fire/parsers/BasicDelimitedTextParser.h:146:26: note: add parentheses around left hand side expression to silence this warning
if (!line.empty() && !line.find("#") == 0) {
^
( )
2 warnings generated.
[ 21%] Building CXX object src/CMakeFiles/fern.dir/kernels.cpp.o
[ 26%] Building CXX object src/CMakeFiles/fern.dir/main.cpp.o
**In file included from /Users/Dan/Desktop/Research/FERN/fernRefactor/fern/src/main.cpp:39:
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/src/DefaultStepper.h:143:28: error: call to 'abs' is ambiguous
fern_real massChecker = std::abs(sumXLast - sumX);
^~~~~~~~
/usr/include/stdlib.h:129:6: note: candidate function
int abs(int) __pure2;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long abs( long __x) _NOEXCEPT {return labs(__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT {return llabs(__x);}
^
In file included from /Users/Dan/Desktop/Research/FERN/fernRefactor/fern/src/main.cpp:39:
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/src/DefaultStepper.h:145:8: error: call to 'abs' is ambiguous
if (std::abs(test2) > std::abs(test1) && massChecker > network.massTol) {
^~~~~~~~
/usr/include/stdlib.h:129:6: note: candidate function
int abs(int) __pure2;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long abs( long __x) _NOEXCEPT {return labs(__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT {return llabs(__x);}
^
In file included from /Users/Dan/Desktop/Research/FERN/fernRefactor/fern/src/main.cpp:39:
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/src/DefaultStepper.h:145:26: error: call to 'abs' is ambiguous
if (std::abs(test2) > std::abs(test1) && massChecker > network.massTol) {
^~~~~~~~
/usr/include/stdlib.h:129:6: note: candidate function
int abs(int) __pure2;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long abs( long __x) _NOEXCEPT {return labs(__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT {return llabs(__x);}
^
In file included from /Users/Dan/Desktop/Research/FERN/fernRefactor/fern/src/main.cpp:39:
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/src/DefaultStepper.h:146:11: error: use of undeclared identifier 'fmax'
dt = fmax( network.massTol / massChecker, downbumper);
^
/Users/Dan/Desktop/Research/FERN/fernRefactor/fern/src/DefaultStepper.h:148:31: error: use of undeclared identifier 'fmax'
dt = (network.massTol / (fmax(massChecker, upbumper)));
^
5 errors generated.

This .ini file for 150-isotope network results in a segmentation violation. Pls, Jay? How to .ini?

[network]
numSpecies = 150
numReactions = 1604
numReactionGroups = 742
massTol = 1.0e-7
fluxFrac = 0.01
networkFile = ../fern/data/CUDAnet_150.inp
rateFile = ../fern/data/rateLibrary_150.data

[initialConditions]
T9 = 7.0;
startTime = 1.0e-20;
endTime = 1.0e-3;
initialTimeStep = 1.23456789e-22;
density = 1.0e8;