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Upgrade cvode #286

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Upgrade cvode #286

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0f5a498
First attempt at upgrade. Largely works, with small-ish errors, but n…
Jun 13, 2018
50833c2
Correct lapack/blas locations in cvode install.
Jun 14, 2018
b5151d7
Temporarily change cvode location.
Jun 14, 2018
8869c1f
Add missing SUNMATRIX module initialization in the DENSE solver case …
Jun 14, 2018
56b04ee
Move to cvode 3.1.2 and fix FORT_LIB.
Aug 22, 2018
c5da7cd
Fix style in atchem.f90.
Aug 22, 2018
96603ef
Fix style in outputFunctions.f90 (whitespace).
Aug 22, 2018
f53e49b
Explore cvode 3 directory.
Aug 22, 2018
f198757
Remove ls, and fix DYLD_LIBRARY_PATH for new cvode install.
Aug 22, 2018
b24f468
Add changes to output files. None seem to be major, based on looking …
Aug 23, 2018
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2 changes: 1 addition & 1 deletion .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
- numdiff

before_install:
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export DYLD_LIBRARY_PATH=$PWD/cvode/lib:$PWD/openlibm-0.4.1 ; fi
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export DYLD_LIBRARY_PATH=$PWD/cvode-3.1.2-install/lib:$PWD/openlibm-0.4.1 ; fi
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then rm '/usr/local/include/c++' ; fi
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./tools/install/install_cvode.sh $PWD /usr/local/Cellar/[email protected]/4.9.4_1/bin/gfortran-4.9 ; fi
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./tools/install/install_cvode.sh $PWD /usr/bin/gfortran ; fi
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14 changes: 11 additions & 3 deletions src/atchem2.f90
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Expand Up @@ -327,19 +327,27 @@ end subroutine FCVFUN
! SELECT SOLVER TYPE ACCORDING TO FILE INPUT
! SPGMR SOLVER
if ( solverType == 1 ) then
call FCVSPGMR( 0, 1, lookBack, deltaMain, ier )
call FSUNSPGMRINIT( 1, 0, lookBack, ier )
! call FCVSPGMR( 0, 1, lookBack, deltaMain, ier )
call FCVSPILSINIT( ier )
! SPGMR SOLVER WITH BANDED PRECONDITIONER
else if ( solverType == 2 ) then
call FCVSPGMR( 1, 1, lookBack, deltaMain, ier )
call FSUNSPGMRINIT( 1, 1, lookBack, ier )
call FCVSPILSINIT( ier )
call FCVBPINIT( neq, preconBandUpper, preconBandLower, ier )
! call FCVSPGMR( 1, 1, lookBack, deltaMain, ier )
! call FCVBPINIT( neq, preconBandUpper, preconBandLower, ier )
if ( ier /= 0 ) then
write (stderr,*) 'SUNDIALS_ERROR: preconditioner returned ier = ', ier ;
call FCVFREE()
stop
end if
! DENSE SOLVER
else if ( solverType == 3 ) then
call FCVDENSE( neq, ier )
call FSUNDENSEMATINIT( 1, neq, neq, ier )
! call FCVDENSE( neq, ier )
call FSUNDENSELINSOLINIT( 1, ier )
call FCVDLSINIT( ier )
! UNEXPECTED SOLVER TYPE
else
write (stderr,*) 'Error with solverType input, input = ', solverType
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2 changes: 1 addition & 1 deletion src/outputFunctions.f90
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Expand Up @@ -333,7 +333,7 @@ end subroutine outputInstantaneousRates
subroutine outputSpeciesOfInterest( t, specOutReqNames, allSpeciesConcs )
use types_mod
use storage_mod, only : maxSpecLength
use config_functions_mod, only: getConcForSpeciesOfInterest
use config_functions_mod, only : getConcForSpeciesOfInterest
implicit none

real(kind=DP), intent(in) :: t
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2 changes: 2 additions & 0 deletions tools/Makefile
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Expand Up @@ -29,10 +29,12 @@ ifeq ($(TRAVIS_OS_NAME),linux)
# if linux, pass gfortran
FORT_COMP = gfortran
FORT_LIB = ""
CVODELIB = /home/travis/build/AtChem/AtChem2/cvode-3.1.2-install/lib
else
# if macOS, pass homebrew gfortran
FORT_COMP = /usr/local/Cellar/[email protected]/4.9.4_1/bin/gfortran-4.9
FORT_LIB = /usr/local/Cellar/[email protected]/4.9.4_1/lib/gcc/4.9
CVODELIB = /Users/travis/build/AtChem/AtChem2/cvode-3.1.2-install/lib
endif
# else it's not on Travis, so set the fortran compiler as gfortran
else
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10 changes: 5 additions & 5 deletions tools/install/install_cvode.sh
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Expand Up @@ -60,15 +60,15 @@ fi
# Move to provided directory
cd $cvode_dir

wget https://computation.llnl.gov/projects/sundials/download/sundials-2.7.0.tar.gz
tar -zxf sundials-2.7.0.tar.gz
rm sundials-2.7.0.tar.gz
cd sundials-2.7.0/
wget https://computation.llnl.gov/projects/sundials/download/cvode-3.1.2.tar.gz
tar -zxf cvode-3.1.2.tar.gz
rm cvode-3.1.2.tar.gz
cd cvode-3.1.2/

mkdir build
cd build

cmake -DCMAKE_INSTALL_PREFIX=$cvode_dir/cvode \
cmake -DCMAKE_INSTALL_PREFIX=$cvode_dir/cvode-3.1.2-install \
-DCMAKE_C_COMPILER:FILEPATH=gcc \
-DCMAKE_Fortran_COMPILER=$FORT_COMP \
-DBUILD_ARKODE:BOOL=OFF \
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2 changes: 1 addition & 1 deletion travis/tests/full/full.out.cmp
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Expand Up @@ -172,5 +172,5 @@ AtChem2 v1.1-dev
No. nonlinear convergence failures = 0
No. error test failures = 0

Runtime = 10
Runtime = 12
Deallocating memory.
10 changes: 5 additions & 5 deletions travis/tests/full/output/mainSolverParameters.output.cmp
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@@ -1,6 +1,6 @@
t currentStepSize previousStepSize LENRW LENIW NST NFE NETF NCFN NNI NSETUPS QU QCUR NOR LENRWLS LENIWLS LS_FLAG NFELS NJTV NPE NPS NLI NCFL
4.50E+03 1.00000000E+002 1.00000000E+002 58409 50 10 14 0 0 10 2 1 1 0 622761 105 0 0 0 1 0 0 0
5.40E+03 1.00000000E+002 1.00000000E+002 58409 50 19 23 0 0 19 2 1 1 0 622761 105 0 0 0 1 0 0 0
6.30E+03 1.00000000E+002 1.00000000E+002 58409 50 28 32 0 0 28 3 1 1 0 622761 105 0 0 0 1 0 0 0
7.20E+03 1.00000000E+002 1.00000000E+002 58409 50 37 41 0 0 37 3 1 1 0 622761 105 0 0 0 1 0 0 0
8.10E+03 1.00000000E+002 1.00000000E+002 58409 50 46 50 0 0 46 4 1 1 0 622761 105 0 0 0 1 0 0 0
4.50E+03 1.00000000E+002 1.00000000E+002 58409 50 10 14 0 0 10 2 1 1 0 634429 117 0 0 0 1 0 0 0
5.40E+03 1.00000000E+002 1.00000000E+002 58409 50 19 23 0 0 19 2 1 1 0 634429 117 0 0 0 1 0 0 0
6.30E+03 1.00000000E+002 1.00000000E+002 58409 50 28 32 0 0 28 3 1 1 0 634429 117 0 0 0 1 0 0 0
7.20E+03 1.00000000E+002 1.00000000E+002 58409 50 37 41 0 0 37 3 1 1 0 634429 117 0 0 0 1 0 0 0
8.10E+03 1.00000000E+002 1.00000000E+002 58409 50 46 50 0 0 46 4 1 1 0 634429 117 0 0 0 1 0 0 0
6 changes: 3 additions & 3 deletions travis/tests/short/output/mainSolverParameters.output.cmp
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
t currentStepSize previousStepSize LENRW LENIW NST NFE NETF NCFN NNI NSETUPS QU QCUR NOR LENRWLS LENIWLS LS_FLAG NFELS NJTV NPE NPS NLI NCFL
4.35E+04 1.00000000E+002 1.00000000E+002 1129 50 4 8 0 0 4 2 1 1 0 21321 105 0 0 0 1 0 0 0
4.38E+04 1.00000000E+002 1.00000000E+002 1129 50 7 11 0 0 7 2 1 1 0 21321 105 0 0 0 1 0 0 0
4.41E+04 1.00000000E+002 1.00000000E+002 1129 50 10 14 0 0 10 2 1 1 0 21321 105 0 0 0 1 0 0 0
4.35E+04 1.00000000E+002 1.00000000E+002 1129 50 4 8 0 0 4 2 1 1 0 21533 117 0 0 0 1 0 0 0
4.38E+04 1.00000000E+002 1.00000000E+002 1129 50 7 11 0 0 7 2 1 1 0 21533 117 0 0 0 1 0 0 0
4.41E+04 1.00000000E+002 1.00000000E+002 1129 50 10 14 0 0 10 2 1 1 0 21533 117 0 0 0 1 0 0 0
6 changes: 3 additions & 3 deletions travis/tests/short_dense/output/mainSolverParameters.output.cmp
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
t currentStepSize previousStepSize LENRW LENIW NST NFE NETF NCFN NNI NSETUPS QU QCUR NOR LENRWLS LENIWLS LS_FLAG NFELS NJE
4.35E+04 1.00000000E+002 1.00000000E+002 1129 50 4 8 0 0 4 2 1 1 0 21632 104 0 104 1
4.38E+04 1.00000000E+002 1.00000000E+002 1129 50 7 11 0 0 7 2 1 1 0 21632 104 0 104 1
4.41E+04 1.00000000E+002 1.00000000E+002 1129 50 10 14 0 0 10 2 1 1 0 21632 104 0 104 1
4.35E+04 1.00000000E+002 1.00000000E+002 1129 50 4 8 0 0 4 2 1 1 0 10920 214 0 104 1
4.38E+04 1.00000000E+002 1.00000000E+002 1129 50 7 11 0 0 7 2 1 1 0 10920 214 0 104 1
4.41E+04 1.00000000E+002 1.00000000E+002 1129 50 10 14 0 0 10 2 1 1 0 10920 214 0 104 1
20 changes: 10 additions & 10 deletions travis/tests/short_end_of_day/output/mainSolverParameters.output.cmp
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
t currentStepSize previousStepSize LENRW LENIW NST NFE NETF NCFN NNI NSETUPS QU QCUR NOR LENRWLS LENIWLS LS_FLAG NFELS NJTV NPE NPS NLI NCFL
8.49E+04 1.00000000E+002 1.00000000E+002 1129 50 4 8 0 0 4 2 1 1 0 21321 105 0 0 0 1 0 0 0
8.52E+04 1.00000000E+002 1.00000000E+002 1129 50 7 11 0 0 7 2 1 1 0 21321 105 0 0 0 1 0 0 0
8.55E+04 1.00000000E+002 1.00000000E+002 1129 50 10 14 0 0 10 2 1 1 0 21321 105 0 0 0 1 0 0 0
8.58E+04 1.00000000E+002 1.00000000E+002 1129 50 13 17 0 0 13 2 1 1 0 21321 105 0 0 0 1 0 0 0
8.61E+04 1.00000000E+002 1.00000000E+002 1129 50 16 20 0 0 16 2 1 1 0 21321 105 0 0 0 1 0 0 0
8.64E+04 1.00000000E+002 1.00000000E+002 1129 50 19 23 0 0 19 2 1 1 0 21321 105 0 0 0 1 0 0 0
8.67E+04 1.00000000E+002 1.00000000E+002 1129 50 22 26 0 0 22 3 1 1 0 21321 105 0 0 0 1 0 0 0
8.70E+04 1.00000000E+002 1.00000000E+002 1129 50 25 29 0 0 25 3 1 1 0 21321 105 0 0 0 1 0 0 0
8.73E+04 1.00000000E+002 1.00000000E+002 1129 50 28 32 0 0 28 3 1 1 0 21321 105 0 0 0 1 0 0 0
8.76E+04 1.00000000E+002 1.00000000E+002 1129 50 31 35 0 0 31 3 1 1 0 21321 105 0 0 0 1 0 0 0
8.49E+04 1.00000000E+002 1.00000000E+002 1129 50 4 8 0 0 4 2 1 1 0 21533 117 0 0 0 1 0 0 0
8.52E+04 1.00000000E+002 1.00000000E+002 1129 50 7 11 0 0 7 2 1 1 0 21533 117 0 0 0 1 0 0 0
8.55E+04 1.00000000E+002 1.00000000E+002 1129 50 10 14 0 0 10 2 1 1 0 21533 117 0 0 0 1 0 0 0
8.58E+04 1.00000000E+002 1.00000000E+002 1129 50 13 17 0 0 13 2 1 1 0 21533 117 0 0 0 1 0 0 0
8.61E+04 1.00000000E+002 1.00000000E+002 1129 50 16 20 0 0 16 2 1 1 0 21533 117 0 0 0 1 0 0 0
8.64E+04 1.00000000E+002 1.00000000E+002 1129 50 19 23 0 0 19 2 1 1 0 21533 117 0 0 0 1 0 0 0
8.67E+04 1.00000000E+002 1.00000000E+002 1129 50 22 26 0 0 22 3 1 1 0 21533 117 0 0 0 1 0 0 0
8.70E+04 1.00000000E+002 1.00000000E+002 1129 50 25 29 0 0 25 3 1 1 0 21533 117 0 0 0 1 0 0 0
8.73E+04 1.00000000E+002 1.00000000E+002 1129 50 28 32 0 0 28 3 1 1 0 21533 117 0 0 0 1 0 0 0
8.76E+04 1.00000000E+002 1.00000000E+002 1129 50 31 35 0 0 31 3 1 1 0 21533 117 0 0 0 1 0 0 0
6 changes: 3 additions & 3 deletions travis/tests/short_ext1/output/environmentVariables.output.cmp
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@@ -1,4 +1,4 @@
t M TEMP PRESS RH H2O DEC BLHEIGHT DILUTE JFAC ROOFOPEN RO2
4.350000E+004 2.445710E+019 3.000000E+002 1.013000E+003 -1.000000E+000 7.020000E+017 1.925804E-001 -1.000000E+000 -1.000000E+000 1.000000E+000 1.000000E+000 1.702440E+007
4.380000E+004 2.445710E+019 3.000000E+002 1.013000E+003 -1.000000E+000 7.020000E+017 1.925804E-001 -1.000000E+000 -1.000000E+000 1.000000E+000 1.000000E+000 2.499414E+007
4.410000E+004 2.445710E+019 3.000000E+002 1.013000E+003 -1.000000E+000 7.020000E+017 1.925804E-001 -1.000000E+000 -1.000000E+000 1.000000E+000 1.000000E+000 3.245431E+007
4.350000E+004 2.445710E+019 3.000000E+002 1.013000E+003 -1.000000E+000 7.020000E+017 1.925804E-001 -1.000000E+000 -1.000000E+000 1.000000E+000 1.000000E+000 1.702469E+007
4.380000E+004 2.445710E+019 3.000000E+002 1.013000E+003 -1.000000E+000 7.020000E+017 1.925804E-001 -1.000000E+000 -1.000000E+000 1.000000E+000 1.000000E+000 2.499424E+007
4.410000E+004 2.445710E+019 3.000000E+002 1.013000E+003 -1.000000E+000 7.020000E+017 1.925804E-001 -1.000000E+000 -1.000000E+000 1.000000E+000 1.000000E+000 3.245428E+007
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