GNU Fortran compiler

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:

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
-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
	Special compiler settings
-fdefault-real-8	This option tells the compiler to treat variables that are declared as REAL as REAL*8 NOTE: This option is not used globally, but is only applied to certain indidvidual files (mostly from third-party codes like ISORROPIA. Current GEOS-Chem programming practice is to use either REAL*4 or REAL*8 instead of REAL, which avoids confusion.	Used as needed
-freal-4-real-8	This option tells the compiler to treat variables that are declared as REAL as REAL*8 NOTE: This option is not used globally, but is only applied to certain indidvidual files (mostly from third-party codes like ISORROPIA. Current GEOS-Chem programming practice is to use either REAL*4 or REAL*8 instead of REAL, which avoids confusion.	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
-fbacktrace	This option tells the compiler to generate extra information in the object file to provide source file traceback information when a severe error occurs at run time. When the severe error occurs, source file, routine name, and line number correlation information is displayed along with call stack hexadecimal addresses (program counter trace). This option increases the size of the executable program, but has no impact on run-time execution speeds. It functions independently of the debug option.	TRACEBACK=yes
-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=yes
-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=yes
-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.	FPE=yes
-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.	FPE=yes
-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=yes
-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=yes
-Wall	Enables some common compiler warnings that you probably would not enable out unless you were debugging.	DEBUG=yes
-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=yes
-Wconversion	Warn about implicit conversions that are likely to change the value of the expression after conversion. Implied by -Wall.	DEBUG=yes
-Wextra	-Wextra Enables some warning options for usages of language features which may be problematic. This currently includes -Wcompare-reals and -Wunused-parameter.	DEBUG=yes

--Bob Yantosca (talk) 21:55, 21 September 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 
-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 
-fopenmp -mcmodel=medium -g -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

Module in GeosCore

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

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_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	#if defined( LINUX_GFORTRAN ) 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 #else  ! This code is preblematic in Gfortran.  ! Investigate rewriting it for IFORT with  ! the DO loops (sde, bmy, 9/21/16) WHERE ( REGFRACS > MAXFRACS ) MAXFRACS = REGR_4D INDECES = IVAL END WHERE #endif # For now, rewrite the offending where statement as # individual DO loops. Need to still test that this # does not introduce any changes with ifort.
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 module 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 with 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 with in a FORMAT statement.