Difference between revisions of "GNU Fortran compiler"
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=== Using the module command to load GNU Fortran and related libraries === | === Using the module command to load GNU Fortran and related libraries === | ||
| − | On | + | On Unix computer systems, you can use [[Installing libraries for GEOS-Chem#Using modules|a module manager such as Lmod]] to load the GNU Fortran compiler library (and its dependencies) into your Unix environment. For example, we use the following commands on the Harvard cluster (odyssey.rc.fas.harvard.edu): |
| − | # These commands load GNU Fortran | + | # These commands load GNU Fortran 8.2.0 on the Harvard "Odyssey" cluster |
| − | module load gcc/ | + | module load gcc/8.2.0-fasrc01 |
| − | module load netcdf/4. | + | module load openmpi/3.1.1-fasrc01 |
| + | module load netcdf/4.1.3-fasrc02 | ||
You can ask your IT staff what the corresponding commands would be on your particular cluster. | You can ask your IT staff what the corresponding commands would be on your particular cluster. | ||
| − | The | + | The Lmod module manager will also define several environment variables for you: |
{| border=1 cellspacing=0 cellpadding=5 | {| border=1 cellspacing=0 cellpadding=5 | ||
| Line 160: | Line 161: | ||
<span style="color:red">'''NOTE: Setting the <tt>OMP_STACKSIZE</tt> environment variable will make it easier to switch between different compilers on your system. The <tt>KMP_STACKSIZE</tt> environment variable only works with the Intel Fortran Compiler but not with GNU Fortran.'''</span> | <span style="color:red">'''NOTE: Setting the <tt>OMP_STACKSIZE</tt> environment variable will make it easier to switch between different compilers on your system. The <tt>KMP_STACKSIZE</tt> environment variable only works with the Intel Fortran Compiler but not with GNU Fortran.'''</span> | ||
| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) | + | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:19, 10 January 2019 (UTC) |
=== Requesting sufficient stack memory for GEOS-Chem === | === Requesting sufficient stack memory for GEOS-Chem === | ||
Revision as of 19:19, 10 January 2019
On this page, we discuss compiling GEOS-Chem with the GNU Fortran compiler (aka gfortran). The GNU Fortran compiler is our recommended open-source compiler for GEOS-Chem.
Contents
- 1 Overview
- 2 Environment settings for GNU Fortran
- 3 Compilation options
- 4 Modifications made to GEOS-Chem for GNU Fortran
- 5 Validation
- 6 Known issues
- 6.1 GNU Fortran seg fault error may be caused by uninitialized variables
- 6.2 Now us ASIN instead of obsolete function ASIND
- 6.3 Now use SIN instead of obsolete function SIND
- 6.4 THREADPRIVATE error in GNU Fortran 5 and higher
- 6.5 GNU Fortran 4.8 and higher is not compatible with Totalview
- 6.6 Compiliation issues with GNU Fortran 8.2.0
Overview
We have added several modifications to facilitate compiling GEOS-Chem with the GNU Fortran (aka gfortran compiler). In the process, we have also corrected some coding issues that were flagged by GNU Fortran. These changes will be added to the v11-01 public release code.
GNU Fortran versions tested with GEOS-Chem
The GEOS-Chem Support Team has experimented using different versions of GNU Fortran to build GEOS-Chem. Here are our results.
| Version | Machine | Status |
|---|---|---|
| gfortran 8.2.0 | odyssey.rc.fas.harvard.edu |
|
| gfortran 7.1.0 | odyssey.rc.fas.harvard.edu |
|
| gfortran 6.3.0 | odyssey.rc.fas.harvard.edu |
|
| gfortran 6.2.0 | odyssey.rc.fas.harvard.edu |
|
| gfortran 5.2.0 | odyssey.rc.fas.harvard.edu |
|
| gfortran 4.8.2 | odyssey.rc.fas.harvard.edu |
|
| gfortran 4.4.7 | odyssey.rc.fas.harvard.edu |
NOTE: Other users have reported issues with gfortran 4.4.7 such as this error: Error: vdiff_mod.F90:193: Internal compiler error: output operand: floating constant misuse which we attribute to an OpenMP issue that was fixed in gfortran 4.7. If you should encounter this issue, try to use a newer compiler version such as 4.8.2 or higher. |
We invite you to test with other versions of GNU Fortran. Please send your results to the GEOS-Chem Support Team.
--Bob Yantosca (talk) 13:59, 21 August 2018 (UTC)
Environment settings for GNU Fortran
Here is some information about how you can customize your Unix environment to use the GNU Fortran compiler.
On Unix computer systems, you can use a module manager such as Lmod to load the GNU Fortran compiler library (and its dependencies) into your Unix environment. For example, we use the following commands on the Harvard cluster (odyssey.rc.fas.harvard.edu):
# These commands load GNU Fortran 8.2.0 on the Harvard "Odyssey" cluster module load gcc/8.2.0-fasrc01 module load openmpi/3.1.1-fasrc01 module load netcdf/4.1.3-fasrc02
You can ask your IT staff what the corresponding commands would be on your particular cluster.
The Lmod module manager will also define several environment variables for you:
| Variable | Expected setting | Description |
|---|---|---|
| FC | gfortran | Name of the GNU Fortran compiler |
| CC | gcc | Name of the GNU C compiler |
| CXX | g++ | Name of the GNU C++ compiler |
| NETCDF_HOME | System-dependent | Path to the root netCDF folder |
| NETCDF_INCLUDE | System-dependent | Path to the netCDF include folder (e.g. $NETCDF_HOME/include) |
| NETCDF_LIB | System-dependent | Path to the netCDF library folder (e.g. $NETCDF_HOME/lib or $NETCDF_HOME/lib64) |
| NETCDF_FORTRAN_HOME | System-dependent | Path to the root netCDF Fortran folder |
| NETCDF_FORTRAN_INCLUDE | System-dependent | Path to the netCDF Fortran include folder (e.g. $NETCDF_FORTRAN_HOME/include) |
| NETCDF_FORTRAN_LIB | System-dependent | Path to the netCDF Fortran library folder (e.g. $NETCDF_FORTRAN_HOME/lib or $NETCDF_FORTRAN_HOME/lib64) |
If these variables are not automatically set by the module command on your system (or if your system does not use the module command:
- Set the FC, CC, and CXX variables automatically in your startup script (e.g. .bashrc or .cshrc).
- Ask your IT staff where the netCDF library paths are located, and set the NETCDF_HOME, NETCDF_INCLUDE, and NETCDF_LIB environment variables accordingly.
Depending on your system, you may find that the netCDF Fortran libraries are installed into a different folder than the rest of the netCDF library files. If this is the case, then the module command should automatically define the NETCDF_FORTRAN_HOME, NETCDF_FORTRAN_INCLUDE, and NETCDF_FORTRAN_LIB environment variables. If not, then ask your IT staff what the proper paths are so that you can set these variables manually.
NOTE: Setting the OMP_STACKSIZE environment variable will make it easier to switch between different compilers on your system. The KMP_STACKSIZE environment variable only works with the Intel Fortran Compiler but not with GNU Fortran.
--Bob Yantosca (talk) 19:19, 10 January 2019 (UTC)
Requesting sufficient stack memory for GEOS-Chem
In order to run GEOS-Chem with GNU Fortran, you must request the maximum amount of stack memory in your Unix environment. (The stack memory is where local automatic variables and temporary !$OMP PRIVATE variables will be created.) Add the following lines to your system startup file:
| If you use bash. add this to your .bashrc file |
If you use csh or tcsh, add this to your .cshrc file |
|---|---|
ulimit -s unlimited export OMP_STACKSIZE=500m |
limit stacksize unlimited setenv OMP_STACKSIZE 500m |
The ulimit -s unlimited (for bash) or limit stacksize unlimited commands tell the Unix shell to use the maximum amount of stack memory available.
The environment variable OMP_STACKSIZE must also be set to a very large number. In this example, we are nominally requesting 500 MB of memory. But in practice, this will tell the GNU Fortran compiler to use the maximum amount of stack memory available on your system. The value 500m is a good round number that is larger than the amount of stack memory on most computer clusters, but you can change this if you wish.
--Bob Yantosca (talk) 19:26, 4 October 2016 (UTC)
Compilation options
The sections below contain useful information about the GNU Fortran compiler options that are used for GEOS-Chem.
Optimization options
Please see the Optimize Options section of the GNU Compiler Collection manual for detailed information about GNU Fortran's optimization settings.
The default GNU Fortran optimization settings for GEOS-Chem are: -O3 -funroll-loops.
--Bob Yantosca (talk) 22:01, 21 September 2016 (UTC)
Debugging options
Please see the Debugging Options section of the GNU Compiler Collection manual for detailed information about GNU Fortran's debugging settings.
--Bob Yantosca (talk) 20:16, 22 September 2016 (UTC)
List of commonly-used compilation options
Here are the GNU Fortran compilation options currently used by GEOS-Chem. For a complete list of options, please see the GNU Fortran (v4.8.2) manual.
| Option | Description | How invoked in GEOS-Chem? |
|---|---|---|
| Normal compiler settings | ||
| -cpp | Turns on the C-preprocessor, to evaluate #if and #define statements in the source code. | Default setting |
| -fautomatic | This option places local variables (scalars and arrays of all types), except those declared as SAVE, on the run-time stack. It is as if the variables were declared with the AUTOMATIC attribute. It does not affect variables that have the SAVE attribute or ALLOCATABLE attribute, or variables that appear in an EQUIVALENCE statement or in a common block. | Default setting |
| -fconvert-big-endian | Specifies that the format will be big endian for integer data and big endian IEEE floating-point for real and complex data. This only affects file I/O to/from binary files (such as binary punch files) but not ASCII, netCDF, or other file formats. | Default setting |
| -fno-align-commons | Prevents the compiler from padding bytes anywhere in common blocks and structures. Padding can affect numerical precision. | Default setting |
| -fopenmp | Enables OpenMP parallelization commands. | Default setting |
| -funroll-loops | Typically improves performance on code using iterative DO loops by unrolling them and is probably generally appropriate for Fortran, though it is not turned on at any optimization level. Note that outer loop unrolling isn't done specifically; decisions about whether to unroll a loop are made on the basis of its instruction count.
Also, no `loop discovery' is done, so only loops written with DO benefit from loop optimizations, including—but not limited to—unrolling. Loops written with IF and GOTO are not currently recognized as such. This option unrolls only iterative DO loops, not DO WHILE loops. |
Default setting |
| -march=native | This selects the CPU to generate code for at compilation time by determining the processor type of the compiling machine. Using -march=native enables all instruction subsets supported by the local machine (hence the result might not run on different machines). We use this option for compiling GEOS-Chem because it is the most portable.
|
M_ARCH=native |
| -O3 | Performs nearly all supported optimizations that do not involve a space-speed tradeoff, plus a few more optimizations for function inlining and vectorization. For more information, please see the Optimize Options section of the GNU Compiler Collection manual. | Default setting |
| -std=legacy | Tells GNU Fortran not to halt compilation when encountering code that does not adhere to the Fortran 95, 2003, or 2008 standards. Gfortran is a much stricter compiler, so turning this option on will tell Gfortran to be more lenient. | Default setting |
| -w | Turns off most informational warnings. | Default setting |
| -fbacktrace | When a serious runtime error is encountered or a deadly signal is emitted (segmentation fault, illegal instruction, bus error, floating-point exception, and the other POSIX signals that have the action "dump core"), this option will tell the Fortran runtime library to output a backtrace of the error. (The complementary option -fno-backtrace disables the backtrace generation._ This option only has influence for compilation of the Fortran main program. | Default setting |
| Special compiler settings | ||
| -fdefault-real-8 | This option tells the compiler to treat elevate REAL variables to REAL*8. As a side-effect, it will also elevate REAL*8 (or DOUBLE PRECISION) variables to REAL*16.
NOTE: This option is not used globally, but is only applied to certain indidvidual files (mostly from third-party codes like ISORROPIA. |
Used as needed |
| -fdefault-double-8 | Using -fdefault-real-8 -fdefault-double-8 together will elevate REAL variables to REAL*8, but will leave REAL*4 variables unchanged. It will also leave REAL*8 or DOUBLE PRECISION variables unchanged.
NOTE: This option is not used globally, but is only applied to certain indidvidual files (mostly from third-party codes like ISORROPIA. |
Used as needed |
| -mcmodel=medium | This option is used to tell Gfortran to use more than 2GB of static memory. This avoids a specific type of memory error that can occur if you compile GEOS-Chem for use with an extremely high-resolution grid (e.g. 0.25° x 0.3125° nested grid). | Default setting |
| Settings only used for debugging | ||
| -fcheck-array-temporaries | Checks to see if any array temporaries are created. Depending on how you write your subroutine and function calls, the compiler may need to create a temporary array to hold the values in the array before it passes them to the subroutine. For detailed information, please see our Passing array arguments efficiently in GEOS-Chem wiki page. | DEBUG=y |
| -fcheck-bounds | Check for array-out-of-bounds errors. This is invoked when you compile GEOS-Chem with the BOUNDS=yes Makefile option. NOTE: Only use this option -fcheck-bounds for debugging, as this option will cause GEOS-Chem to execute more slowly! | BOUNDS=y |
| -ffpe-trap=invalid,zero,overflow | This option will cause GEOS-Chem to halt when floating-point errors are encountered. This can happen if an equation results in a denormal value, e.g. NaN, or +/-Infinity. Common causes of floating-point errors are divisions where the denominator becomes zero. | FPEX=y or FPE=y |
| -finit-real-snan | This option will set local automatic variables to a signaling NaN. This will make it easier for the compiler to detect undefined variables. | FPEX=y or FPE=y |
| -g | Tells the compiler to generate full debugging information in the object file. This will cause a debugger (like Totalview) to display the actual lines of source code, instead of hexadecimal addresses (which is gibberish to anyone except hardware engineers). | DEBUG=y |
| -gdwarf-2 | Tells the compiler to generate full debugging information using the DWARF-2 library standard. | DEBUG=y |
| -gdwarf-2 | Tells the compiler to strictly adhere to the DWARF-2 debugging library standard. | DEBUG=y |
| -O0 | Turns off all optimization. Source code instructions (e.g. DO loops, IF blocks) and numerical expressions are evaluated in precisely the order in which they are listed, without being internally rewritten by the optimizer. This is necessary for using a debugger (like Totalview). | DEBUG=y |
| -Wall | Enables some common compiler warnings that you probably would not enable out unless you were debugging. | DEBUG=y |
| -Warray-temporaries | Warn about array temporaries generated by the compiler. The information generated by this warning is sometimes useful in optimization, in order to avoid
such temporaries. Used in conjunction with -fcheck-array-temporaries. |
DEBUG=y |
| -Wconversion | Warn about implicit conversions that are likely to change the value of the expression after conversion. Implied by -Wall. | DEBUG=y |
| -Wextra | -Wextra Enables some warning options for usages of language features which may be problematic. This currently includes -Wcompare-reals and -Wunused-parameter. | DEBUG=y |
--Bob Yantosca (talk) 20:18, 9 December 2016 (UTC)
Typical settings for a GEOS-Chem simulation
The normal GEOS-Chem build uses the following Gfortran compiler flags:
-cpp -w -std=legacy -fautomatic -fno-align-commons -fconvert=big-endian -fno-range-check -march=native -fopenmp -mcmodel=medium -O3 -funroll-loops
whereas a debugging run (meant to execute in a debugger such as TotalView) will typically use these flags:
-cpp -w -std=legacy -fautomatic -fno-align-commons -fconvert=big-endian -fno-range-check -march=native -fopenmp -mcmodel=medium -g gdwarf-2 -gstrict-dwarf -O0 -Wall -Wextra -Warray-temporaries -Wconversion -fcheck-array-temporaries -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow, -finit-real=snan
--Bob Yantosca (talk) 20:15, 22 September 2016 (UTC)
Modifications made to GEOS-Chem for GNU Fortran
The following tables list the modifications that had to be made in order to compile GEOS-Chem with GNU Fortran. These fixes were standardized into GEOS-Chem between v11-01 and the 12.0.0 (aka v11-02-final) versions.
Module in GeosCore
| Module | Code removed (in RED) | Code added (in GREEN) |
|---|---|---|
carbon_mod.F |
GLOB_DARO2(I,J,L,:,JHC-5) = DELHC(:) . . . GLOB_DARO2(I,J,L,:,4) = DELHC(:) |
GLOB_DARO2(I,J,L,1:2,JHC-5) = DELHC(1:2) . . . GLOB_DARO2(I,J,L,1:2,4) = DELHC(1:2) # Now only copy the 1st 2 elements of DELHC # into GLOB_DARO2, which avoids an array-size mismatch |
convection_mod.F |
IF ( AER == .TRUE. ) THEN
|
IF ( AER ) THEN |
diag3.F |
(Input_Opt%LSKYRAD(2).EQ.TRUE.)) . . . (Input_Opt%LSKYRAD(1).EQ.TRUE.)) |
(Input_Opt%LSKYRAD(2).EQV.TRUE.)) . . . (Input_Opt%LSKYRAD(1).EQV.TRUE.)) |
diag_mod.F |
INTEGER, ALLOCATABLE :: AD71_COUNT
INTEGER, ALLOCATABLE :: AD71_HRCT
INTEGER, ALLOCATABLE :: AD71_LHR
INTEGER, ALLOCATABLE :: AD71_LDAY
|
INTEGER :: AD71_COUNT
INTEGER :: AD71_HRCT
INTEGER :: AD71_LHR
INTEGER :: AD71_LDAY
# Scalar variables cannot be declared ALLOCATABLE.
|
diag48_mod.F |
(Input_Opt%LSKYRAD(2).EQ.TRUE.)) . . . (Input_Opt%LSKYRAD(1).EQ.TRUE.)) |
(Input_Opt%LSKYRAD(2).EQV.TRUE.)) . . . (Input_Opt%LSKYRAD(1).EQV.TRUE.)) |
emissions_mod.F90 |
CALL EMISSCARBON( ... etc ... ) IF ( RC /= GC_SUCCESS ) RETURN |
IF ( Input_Opt%ITS_A_FULLCHEM_SIM .or. & Input_Opt%ITS_AN_AEROSOL_SIM ) THEN CALL EMISSCARBON( ... etc ... ) IF ( RC /= GC_SUCCESS ) RETURN ENDIF # Need to prevent EMISSCARBON from being called # for simulations without carbon aerosols |
flexchem_mod.F90 |
write(*,'(i,a3,a85)') D,' | ',EQN_NAMES(D) |
WRITE( 6, '(i8,a3,a85)' ) D,' | ',EQN_NAMES(D)
|
geosfp_read_mod.F90 |
INTEGER, SAVE :: first = .TRUE.
|
LOGICAL, SAVE :: first = .TRUE.
|
hcoi_gc_diagn_mod.F90 |
IF ( YesOrNo == .FALSE. ) THEN
|
IF ( YesOrNo .eqv. FALSE ) THEN
|
hcoi_gc_diagn_mod.F90 |
IF ( ( ExtState%DustDead .OR.
ExtState%DustGinoux ) .AND. &
|
Is_DustDead = ( ExtState%DustDead )
Is_DustGinoux = ( ExtState%DustGinoux )
. . .
IF ( ( Is_DustDead .OR. Is_DustGinoux ) .AND. &
|
hcoi_gc_main_mod.F90 |
IF ( Input_Opt%LUCX /= LTMP ) THEN . . . IF ( Input_Opt%LSCHEM /= LTMP ) THEN . . . IF ( Input_Opt%LCHEM /=. LTMP .and. |
IF ( Input_Opt%LUCX .neqv. LTMP ) THEN . . . IF ( Input_Opt%LSCHEM .neqv. LTMP ) THEN . . . IF ( Input_Opt%LCHEM .neqv./ LTMP .and. |
input_mod.F |
READ( SUBSTRS(1:N), '(i)') CFCYEAR
. . .
write(MSG,'(I,a,L)') '<>', Input_Opt%TS_DYN, ...
. . .
Input_Opt%ND63_TRACERS(1:ND63) = TRACERS(1:N_ND63)
. . .
IF ( LCH4BUD .EQ. .TRUE. ) THEN
|
READ( SUBSTRS(1:N), '(i4)') CFCYEAR . . . write(MSG,'(I8,a,L)') '<>', Input_Opt%TS_DYN, ... . . . Input_Opt%ND63_TRACERS(1:N_ND63) = TRACERS(1:N_ND63) . . . IF ( LCH4BUD ) THEN |
isoropiaII_mod.F |
#IF !defined ( USE_REAL_8 ) HNO3_sav(I,J,L) = SNGL(HNO3_UGM3) #ELIF HNO3_sav(I,J,L) = HNO3_UGM3 #ENDIF |
#if !defined( USE_REAL_8 ) HNO3_sav(I,J,L) = SNGL(HNO3_UGM3) #else HNO3_sav(I,J,L) = HNO3_UGM3 #endif |
ocean_mercury_mod.F |
IF ( ND03 .and. NN == ID_Hg_tot )
|
IF ( ( ND03 > 0 ) .and. ( NN == ID_Hg_tot ) ) # Use parentheses to cast to LOGICAL type |
merra2_read_mod.F90 |
INTEGER, SAVE :: first = .TRUE.
|
LOGICAL, SAVE :: first = .TRUE.
|
ndxx_setup.F |
INTEGER :: IT_IS_A_CH3I_SIM INTEGER :: IT_IS_A_FULLCHEM_SIM INTEGER :: IT_IS_A_MERCURY_SIM INTEGER :: IT_IS_A_TAGO3_SIM INTEGER :: IT_IS_A_H2HD_SIM |
LOGICAL :: IT_IS_A_CH3I_SIM LOGICAL :: IT_IS_A_FULLCHEM_SIM LOGICAL :: IT_IS_A_MERCURY_SIM LOGICAL :: IT_IS_A_TAGO3_SIM LOGICAL :: IT_IS_A_H2HD_SIM |
ndxx_setup.F |
IF ( ALLOCATED( AD71_COUNT ) ) DEALLOCATE( AD71_COUNT )
IF ( ALLOCATED( AD71_HRCT ) ) DEALLOCATE( AD71_HRCT )
IF ( ALLOCATED( AD71_LDAY ) ) DEALLOCATE( AD71_LDAY )
IF ( ALLOCATED( AD71_LHR ) ) DEALLOCATE( AD71_LHR )
|
|
seasalt_mod.F |
IF (DMID(ID) .ge. R0*2e+0_fp .and. ...
& THEN
|
IF ( DMID(ID) .ge. R0*2e+0_fp .and.
& DMID(ID) .le. R1*2e+0_fp ) THEN
# Break IF statement into 2 lines
|
seasalt_mod.F |
IF ( LMPOA > 0 ) THEN
|
IF ( LMPOA ) THEN |
strat_chem_mod.F90 |
'A3O2', 'ACET', etc.
|
'A3O2 ', 'ACET ', etc.
# All strings in array constructors must
# have the same number of spaces
|
strat_chem_mod.F90 |
TYPE(BrPointers) :: BrPtrDay(6)
TYPE(BrPointers) :: BrPtrNight(6)
|
TYPE(BrPointers), POINTER :: BrPtrDay(:) TYPE(BrPointers), POINTER :: BrPtrNight(:) . . . ! BrPtrDay and BrPtrNight have to be allocated dynamically ! because they are pointers (bmy, 10/3/16) ALLOCATE( BrPtrDay ( 6 ), STAT=errCode ) ALLOCATE( BrPtrNight( 6 ), STAT=errCode ) . . . IF ( ASSOCIATED( BrPtrDay ) ) DEALLOCATE( BrPtrDay ) IF ( ASSOCIATED( BrPtrNight ) ) DEALLOCATE( BrPtrNight ) # Dynamically allocate the BrPtrDay and BrPtrNight arrays # so as to not have to declare them SAVEd. |
ucx_mod.F90 |
JDIF_OUT = SIND(JMAX_OUT)-SIND(JMIN_OUT) . . . JDIF_TMP = SIND(JMAX_TMP)-SIND(JMIN_TMP) |
USE PhysConstants, ONLY : PI_180 . . . JDIF_OUT = SIN( JMAX_OUT * PI_180 ) & - SIN( JMIN_OUT * PI_180 ) . . . JDIF_TMP = SIN( JMAX_TMP * PI_180 ) & - SIN( JMIN_TMP * PI_180 ) # Remove unsupported SIND function |
--Bob Yantosca (talk) 19:45, 28 September 2016 (UTC)
Modules in GeosUtil
| Module | Code removed (in RED) | Code added (in GREEN) |
|---|---|---|
error_mod.F |
#if defined( LINUX_IFORT ) |
#if defined( LINUX_IFORT ) || defined( LINUX_GFORTRAN )
|
geos_timers_mod.F |
IF ( (SavedTimers(TimerLoc)%ENABLED) .eq. .true.)
|
IF ( SavedTimers(TimerLoc)%ENABLED ) |
henry_coeffs_mod.F |
'H2O2', ! Jacob et al. 2000
'CH3I', ! Moore et al. 1995
'DMS', ! De Bruyn et al. 1995
'ACET' )/ ! Benkelberg et al 1995
|
'H2O2', ! Jacob et al. 2000 'CH3I', ! Moore et al. 1995 'DMS ', ! De Bruyn et al. 1995 'ACET' )/ ! Benkelberg et al 1995 # All strings in an array constructor # must have the same number of spaces |
--Bob Yantosca (talk) 19:13, 28 September 2016 (UTC)
Modules in Headers
| Module | Code removed (in RED) | Code added (in GREEN) |
|---|---|---|
input_opt_mod.F90 |
INTEGER :: LND51_HDF . . . INTEGER :: LND51b_HDF . . . INTEGER :: LWINDO_SE . . . INTEGER :: LWINDO_CU |
LOGICAL :: LND51_HDF . . . LOGICAL :: LND51b_HDF . . . LOGICAL :: LWINDO_SE . . . LOGICAL :: LWINDO_CU |
--Bob Yantosca (talk) 19:49, 28 September 2016 (UTC)
Modules in HEMCO/Core
| Module | Code removed (in RED) | Code added (in GREEN) |
|---|---|---|
hco_calc_mod.F90 |
IF ( UseConc /= Dct%Dta%IsConc ) THEN
|
IF ( UseConc .neqv. Dct%Dta%IsConc ) THEN # Use .eqv. and .neqv. instead of == or /= # when comparing LOGICAL variables directly. |
hco_datacont_mod.F90 |
TYPE(ListCont), POINTER :: TmpLct => NULL()
|
TYPE(ListCont), POINTER :: TmpLct
. . .
TmpLct => NULL()
|
hco_diagn_mod.F90 |
INTERFACE Diagn_Update MODULE PROCEDURE Diagn_UpdateSP MODULE PROCEDURE Diagn_UpdateDP END INTERFACE # Removed DiagnUpdateSP and DiagnUpdateDP # which used OPTIONAL arguments |
PRIVATE :: Diagn_UpdateSp0d PRIVATE :: Diagn_UpdateSp0d PRIVATE :: Diagn_UpdateSp2d PRIVATE :: Diagn_UpdateSp3d PRIVATE :: Diagn_UpdateDp0d PRIVATE :: Diagn_UpdateDp2d PRIVATE :: Diagn_UpdateDp3d ... INTERFACE Diagn_Update MODULE PROCEDURE Diagn_UpdateSp0d MODULE PROCEDURE Diagn_UpdateSp2d MODULE PROCEDURE Diagn_UpdateSp3d MODULE PROCEDURE Diagn_UpdateDp0d MODULE PROCEDURE Diagn_UpdateDp2d MODULE PROCEDURE Diagn_UpdateDp3d END INTERFACE # Added new routines DiagnUpdateSp* and DiagUpdateDp* # to avoid using OPTIONAL arguments in a MODULE INTERFACE |
hco_interp_mod.F90 |
WHERE ( REGFRACS > MAXFRACS )
MAXFRACS = REGR_4D
INDECES = IVAL
END WHERE
|
DO T = 1, NTIME
DO L = 1 ,NLEV
DO J = 1, HcoState%NY
DO I2 = 1, HcoState%NX
IF ( REGFRACS(I2,J,L,T) > MAXFRACS(I2,J,L,T) ) THEN
MAXFRACS(I2,J,L,T) = REGR_4D(I2,J,L,T)
INDECES (I2,J,L,T) = IVAL
ENDIF
ENDDO
ENDDO
ENDDO
ENDDO
|
hco_unit_mod.F90 |
'1', &
'count', &
'unitless', &
etc.
|
'1 ', & 'count ', & 'unitless ', & etc. # All strings in array constructors must have the # same # of spaces or else Gfortran chokes |
--Bob Yantosca (talk) 18:21, 26 September 2016 (UTC)
Modules in HEMCO/Extensions
| Module | Code removed (in RED) | Code added (in GREEN) |
|---|---|---|
hcox_gfed_mod.F90 |
REAL(sp), POINTER :: TmpPtr(:,:) => NULL()
|
REAL(sp), POINTER :: TmpPtr(:,:) ... TmpPtr => NULL() # Setting a pointer to NULL where it is declared # turns the pointer into a SAVEd variable. |
hcox_gfed_mod.F90 |
! Get pointers to GFED3 data
IF ( IsGFED3 ) THEN
.... etc ...
! Get pointers to GFED4 data
ELSEIF ( IsGFED4 ) THEN
... etc ...
ENDIF
! Make sure HUMTROP does not exceed one
WHERE ( HUMTROP > 1.0_sp )
HUMTROP = 1.0_sp
END WHERE
|
! Get pointers to GFED3 data IF ( IsGFED3 ) THEN .... etc ... ! Make sure HUMTROP does not exceed one WHERE ( HUMTROP > 1.0_sp ) HUMTROP = 1.0_sp END WHERE ! Get pointers to GFED4 data ELSEIF ( IsGFED4 ) THEN ... etc ... ENDIF # HUMTROP is only defined for GFED3, so the # WHERE statement should go in the IfGFED3 block. |
hcox_paranox_mod.F90 |
VARS(4) = ASIND( SC5(I,J) ) VARS(5) = ASIND( ExtState%SUNCOS%Arr%Val(I,J) ) |
VARS(4) = ASIN( SC5(I,J) ) / HcoState%Phys%PI_180 VARS(5) = ASIN( ExtState%SUNCOS%Arr%Val(I,J) ) / HcoState%Phys%PI_180 # ASIND is not supported in Gfortran. Use ASIN instead to compute # the arcsin and convert from degrees to radians manually. |
hcox_seasalt_mod.F90 |
ALLOCATE ( NR ( NSALT ), STAT=AS )
IF ( AS/=0 ) THEN
CALL HCO_ERROR( 'Cannot allocate NR', RC )
RETURN
ENDIF
SS_DEN = 2200.d0
ALLOCATE ( SS_DEN ( NSALT ), STAT=AS )
|
ALLOCATE ( NR ( NSALT ), STAT=AS ) IF ( AS/=0 ) THEN CALL HCO_ERROR( 'Cannot allocate NR', RC ) RETURN ENDIF NR = 0 ALLOCATE ( SS_DEN ( NSALT ), STAT=AS ) # Don't refer to SS_DEN before it is allocated |
--Bob Yantosca (talk) 21:07, 26 September 2016 (UTC)
Modules in NcdfUtil
| Module | Code removed (in RED) | Code added (in GREEN) |
|---|---|---|
ncdf_mod.F90 |
PRIVATE :: NC_VAR_WRITE_INT
PRIVATE :: NC_VAR_WRITE_R4
PRIVATE :: NC_VAR_WRITE_R8
|
PRIVATE :: NC_VAR_WRITE_INT_1D
PRIVATE :: NC_VAR_WRITE_INT_2D
PRIVATE :: NC_VAR_WRITE_INT_3D
PRIVATE :: NC_VAR_WRITE_INT_4D
PRIVATE :: NC_VAR_WRITE_R4_1D
PRIVATE :: NC_VAR_WRITE_R4_2D
PRIVATE :: NC_VAR_WRITE_R4_3D
PRIVATE :: NC_VAR_WRITE_R4_4D
PRIVATE :: NC_VAR_WRITE_R8_1D
PRIVATE :: NC_VAR_WRITE_R8_2D
PRIVATE :: NC_VAR_WRITE_R8_3D
PRIVATE :: NC_VAR_WRITE_R8_4D
#Added separate, overloaded routine
# for each combination of array size and INT, REAL*4, REAL*8.
# This avoids using OPTIONAL arguments in overloaded routines,
#which Gfortran hates.
|
ncdf_mod.F90 |
INTERFACE NC_VAR_WRITE
MODULE PROCEDURE NC_VAR_WRITE_INT
MODULE PROCEDURE NC_VAR_WRITE_R4
MODULE PROCEDURE NC_VAR_WRITE_R8
END INTERFACE NC_VAR_WRITE
|
INTERFACE NC_VAR_WRITE
MODULE PROCEDURE NC_VAR_WRITE_INT_1D
MODULE PROCEDURE NC_VAR_WRITE_INT_2D
MODULE PROCEDURE NC_VAR_WRITE_INT_3D
MODULE PROCEDURE NC_VAR_WRITE_INT_4D
MODULE PROCEDURE NC_VAR_WRITE_R4_1D
MODULE PROCEDURE NC_VAR_WRITE_R4_2D
MODULE PROCEDURE NC_VAR_WRITE_R4_3D
MODULE PROCEDURE NC_VAR_WRITE_R4_4D
MODULE PROCEDURE NC_VAR_WRITE_R8_1D
MODULE PROCEDURE NC_VAR_WRITE_R8_2D
MODULE PROCEDURE NC_VAR_WRITE_R8_3D
MODULE PROCEDURE NC_VAR_WRITE_R8_4D
END INTERFACE NC_VAR_WRITE
|
ncdf_mod.F90 |
READ( tUnit(L1:L2), '(i)', IOSTAT=STAT ) tYr READ( tUnit(L1:L2), '(i)', IOSTAT=STAT ) tMt READ( tUnit(L1:L2), '(i)', IOSTAT=STAT ) tDy READ( tUnit(L1:L2), '(i)', IOSTAT=STAT ) tHr READ( tUnit(L1:L2), '(i)', IOSTAT=STAT ) tMn READ( tUnit(L1:L2), '(i)', IOSTAT=STAT ) tSc |
READ( tUnit(L1:L2), '(i4)', IOSTAT=STAT ) tYr READ( tUnit(L1:L2), '(i2)', IOSTAT=STAT ) tMt READ( tUnit(L1:L2), '(i2)', IOSTAT=STAT ) tDy READ( tUnit(L1:L2), '(i2)', IOSTAT=STAT ) tHr READ( tUnit(L1:L2), '(i2)', IOSTAT=STAT ) tMn READ( tUnit(L1:L2), '(i2)', IOSTAT=STAT ) tSc # Gfortran cannot have a generic integer #width in a FORMAT statement. |
ncdf_mod.F90 |
READ( TIMEUNIT(L1:L2), '(i)', IOSTAT=STAT ) YYYY READ( TIMEUNIT(L1:L2), '(i)', IOSTAT=STAT ) MM READ( TIMEUNIT(L1:L2), '(i)', IOSTAT=STAT ) DD READ( TIMEUNIT(L1:L2), '(i)', IOSTAT=STAT ) HH |
READ( TIMEUNIT(L1:L2), '(i4)', IOSTAT=STAT ) YYYY READ( TIMEUNIT(L1:L2), '(i2)', IOSTAT=STAT ) MM READ( TIMEUNIT(L1:L2), '(i2)', IOSTAT=STAT ) DD READ( TIMEUNIT(L1:L2), '(i2)', IOSTAT=STAT ) HH # Gfortran cannot have a generic integer #width in a FORMAT statement. |
--Bob Yantosca (talk) 15:14, 29 September 2016 (UTC)
Fixes for technical issues in the specialty simulation modules
In addition to the modifications listed in the tables above, we fixed a few technical issues were in the various GEOS-Chem specialty simulation modules. These issues were discovered by running complete set of GEOS-Chem unit tests using the GNU Fortran compiler.
- Avoid floating-point exception in OCEAN_MERCURY_READ
- Avoid floating-point error in routine CHEM_POPGP
- Fixed undefined molecular weight of HNO3 in routine SEASALT_CHEM
- Now call subrouine DO_RED_INPLUME after the HEMCO configuration file is read
- Now convert OH to the proper units in the tagged CO simulation
- Allocate the OCCONV array for marine POA simulations
- Replace nonstandard DLOG function with LOG in RRTMG routine
--Lizzie Lundgren (talk) 21:24, 1 November 2016 (UTC)
Validation
In general, the results of GEOS-Chem simulations using GNU Fortran essentially identical results those using the Intel Fortran Compiler. See below for more information.
Also, please see our Timing tests with GEOS-Chem v11-01 wiki page to view results from several GEOS-Chem timing tests using GNU Fortran.
--Bob Yantosca (talk) 17:28, 22 December 2016 (UTC)
Results from the v11-02a 1-month benchmark comparing ifort and gfortran
In order to evaluate the performance of GEOS-Chem using the the free and open source GNU Fortran compiler, we performed two 1-month benchmark simulations for v11-02a.
| Benchmark | Description |
|---|---|
| v11-02a | Uses the Intel Fortran Compiler (ifort 11.1.069) to compile GEOS-Chem |
| v11-02a.GF | Uses the GNU Fortran Compiler (gfortran 6.2.0) to compile GEOS-Chem. |
Both benchmarks yielded essentially identical results in the output (within the expected bounds of numerical noise). This is demonstrated by looking at the mean OH concentration and methyl chloroform lifetimes from both benchmarks:
MEAN OH CONCENTRATION [1e5 molec/cm3/s] --------------------------------------- v11-02a : 12.3128108012973 # with ifort 11.1.069 v11-02a.GF : 12.312863157030780 # with gfortran 6.2.0 % Difference : 0.000425213497755144 MCF LIFETIME w/r/t TROP OH [years] ---------------------------------- v11-02a : 5.1159 # with ifort 11.1.069 v11-02a.GF : 5.1159 # with gfortran 6.2.0 % Difference : 0
Here are the job statistics from both benchmarks:
Machine information (identical for benchmarks w/ ifort and gfortran)
---------------------------------------------------------------------
Machine used : holyjacob01.rc.fas.harvard.edu
CPU Type : Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz
Timing results : v11-02a benchmark v11-02a benchmark
: w/ ifort 11.1.069 w/ gfortran 6.2.0
-------------------------------------------------------------
Number of CPUs : 24 24
Memory used : 5.2038 GB 4.5237 GB
Wall Time : 04:22:54 05:07:26
CPU / Wall Time : 22.5986 17.3599
% of ideal : 94.12 % 72.33 %
We also obtained the wall time spent in each operation of GEOS-Chem. (This is automatically printed out to the log file when you compile GEOS-Chem with the TIMERS=1 option.)
v11-02a with v11-02a with
ifort 11.1.069 gfortran 6.2.0
Timer name hh:mm:ss.SSS hh:mm:ss.SSS
--------------------------------------------------------------------
GEOS-Chem : 04:22:43.009 05:07:21.500
Initialization : 00:00:04.054 00:00:03.875
Timesteps : 04:22:35.931 05:07:17.375
HEMCO : 00:58:35.751 00:51:43.250
All chemistry : 01:27:06.851 01:30:07.750
=> Strat chem : 00:00:33.615 00:00:47.250
=> Gas-phase chem : 01:10:22.802 01:06:20.000
=> All aerosol chem : 00:13:26.291 00:20:09.000
Transport : 00:22:17.939 00:41:05.000
Convection : 00:48:47.117 01:03:08.500
Dry deposition : 00:00:55.591 00:01:09.625
Wet deposition : 00:29:24.046 00:39:15.750
Diagnostics : 00:04:56.912 00:10:05.125
Reading met fields : 00:00:17.359 00:00:15.000
Reading restart file : 00:00:00.304 00:00:00.500
Writing restart file : 00:00:21.253 00:00:04.625
As you can see, several of the operations (listed in RED) are significantly slower with gfortran 6.2.0 than with ifort 11.1.069. A few operations (listed in GREEN) were a little faster in gfortran 6.2.0. We will continue to look for ways to speed up GEOS-Chem when using the GNU Fortran compiler. This may involve optimizing parallel DO loops or fine-tuning the optimization options.
Summary: The benchmark using GNU Fortran yielded essentially identical results to the benchmark using Intel Fortran. This is very encouraging, as it will allow GEOS-Chem development to take place on computational platforms that do not have proprietary compilers (such as Intel Fortran or PGI Fortran), which can be prohibitively expensive to purchase.
--Bob Yantosca (talk) 20:04, 20 April 2017 (UTC)
Known issues
GNU Fortran seg fault error may be caused by uninitialized variables
When using GNU Fortran with the floating-point exception error check flags (FPEX=y or FPE=y), then you should be aware that this will cause uninitialized variables to be set to a signaling NaN value (i.e. IEEE Not-a-Number). Therefore, an uninitialized value (especially an array) could potentially cause an error that is reported as a segmentation fault.
For example, in module GeosCore/pjc_pfix_window_mod.F and GeosCore/tpcore_fvdas_window_mod.F90 we had to zero out several array variables that were uninitialized (in GEOS-Chem v11-02c. These uninitialized arrays were causing the nested-grid simulations to halt with segmentation fault errors.
--Bob Yantosca (talk) 21:38, 11 July 2017 (UTC)
Now us ASIN instead of obsolete function ASIND
In HEMCO module HEMCO/Extensions/hcox_paranox_mod.F90, we had to replace the non-standard function ASIND (which returns the arcsine of an argument in degrees) with the ASIN function (which returns the arcsin in radians). The proper unit conversion was then applied.
The code in RED was deleted:
VARS(4) = ASIND( SC5(I,J) ) VARS(5) = ASIND( ExtState%SUNCOS%Arr%Val(I,J) )
And the code in GREEN was added:
VARS(4) = ASIN( SC5(I,J) ) / HcoState%Phys%PI_180 VARS(5) = ASIN( ExtState%SUNCOS%Arr%Val(I,J) ) / HcoState%Phys%PI_180
This modification does not cause any numerical differences in the output. All difference tests returned identical results.
--Bob Yantosca (talk) 21:00, 30 September 2016 (UTC)
Now use SIN instead of obsolete function SIND
In the UCX chemistry module GeosCore/ucx_mod.F, we had to replace the non-standard function SIND (which returns the sine of an argument in degrees) with the SIN function (which returns the sine in radians). The argument was converted from degrees to radians before being passed to SIN.
The code in RED was deleted:
JDIF_OUT = SIND(JMAX_OUT)-SIND(JMIN_OUT) . . . JDIF_TMP = SIND(JMAX_TMP)-SIND(JMIN_TMP)
And the code in GREEN was added:
USE PhysConstants, ONLY : PI_180 . . . JDIF_OUT = SIN( JMAX_OUT * PI_180 ) & - SIN( JMIN_OUT * PI_180 ) . . . JDIF_TMP = SIN( JMAX_TMP * PI_180 ) & - SIN( JMIN_TMP * PI_180 )
This change causes very small numerical differences, at the level of numerical noise, only in the "Standard" and "UCX" chemical mechanisms. We attribute these differences to conversion between degrees and radians, probably with a different value of PI in each case.
--Bob Yantosca (talk) 21:14, 30 September 2016 (UTC)
THREADPRIVATE error in GNU Fortran 5 and higher
GNU Fortran v5 (actually also in v4.9) and higher seems to not like how the !$OMP THREADPRIVATE statements in the ISORROPIA code are written. It does not let you place a COMMON block name in an !$OMP THREADPRIVATE statement. We are still looking into a workaround for this.
Bob Yantosca wrote:
I tried loading these modules on the holy2a81302 node of Odyssey:
Currently Loaded Modules:
1) git/2.1.0-fasrc01 5) gmp/6.1.1-fasrc02 9) openmpi/1.10.3-fasrc01
2) perl/5.10.1-fasrc04 6) mpfr/3.1.4-fasrc02 10) zlib/1.2.8-fasrc07
3) IDL/8.5.1-fasrc01 7) mpc/1.0.3-fasrc04 11) hdf5/1.8.12-fasrc12
4) ncl/6.1.2 8) gcc/6.1.0-fasrc01 12) netcdf/4.1.3-fasrc09
And then I tried to compile GEOS-Chem with Gfortran 6.1.0, but I got a bunch of these errors:
!$OMP THREADPRIVATE( /CASE/ ) Error: !$OMP THREADPRIVATE statement
is not allowed inside of BLOCK DATA at (1) isrpia.inc:232:72:
This is occurring in a section of 3rd-party, legacy code that is not easily rewritten. I looked on the internet and found this forum on Openmp.org. So it appears that it is not an OpenMP problem, but Gfortran is being petty and pedantic here. Gfortran seems to be very unfriendly to legacy codes.
--Bob Yantosca (talk) 20:37, 28 September 2016 (UTC)
Update: Avoid THREADPRIVATE error by removing COMMON blocks
NOTE: This problem was resolved in GEOS-Chem v11-02.
Seb Eastham has repackaged the ISORROPIA v2.0 code info a Fortran module, which eliminates all COMMON blocks. This structural modification now avoids the error described above. For more information, please see this post on our ISORROPIA II wiki page.
--Bob Yantosca (talk) 20:43, 25 January 2017 (UTC)
GNU Fortran 4.8 and higher is not compatible with Totalview
GNU Fortran 4.8 and higher versions save debugging information to disk using the DWARF library, version 4, by default. This makes code compiled with GNU Fortran incompatible with the Totalview debugger, version 8.8.0.1, which can only accept DWARF v2 or DWARF v3 input. The GEOS-Chem Support Team noticed this on our local computer cluster. We are still looking into a workaround for this.
--Bob Yantosca (talk) 21:39, 30 September 2016 (UTC)
Compiliation issues with GNU Fortran 8.2.0
This update was included in GEOS-Chem 12.0.1, which was released on 24 Aug 2018.
The GEOS-Chem Support Team recently tested GEOS-Chem 12.0.0 with gfortran 8.2.0, which is a recent release of the GNU Compiler Collection. An "out-of-the-box" compilation with gfortran 8.2.0 resulted in two errors:
| Location | Problem | Solution |
|---|---|---|
| GeosCore/ocean_mercury_mod.F90 | Internal compiler error. This error seems related to optimization.
during GIMPLE pass: ccp
ocean_mercury_mod.F:407:0:
USE CMN_SIZE_MOD
internal compiler error: Segmentation fault
|
Compile GeosCore/ocean_mercury_mod.F90 with a lower optmization level.
Use optimization option -O1 instead of the default -O3. |
| GeosCore/ucx_mod.F | Floating-point error caused by uninitialized variables in OpenMP parallel loops. | Comment out all instances of the affected variables.
It turns out these variables are only needed for some debug printout, but are not crucial to the science. |
--Bob Yantosca (talk) 19:00, 20 August 2018 (UTC)
