SMOKE3.5 is based on Intel Ifort error reporting

MMengxin · November 21, 2024, 2:12pm

My basic libraries are all compiled based on the Intel compiler. Now I want to compile the Intel version of SMOKE3.5. I followed the methods in the manual, but I still encountered a lot of trouble.My IOAPI library and NetCDF library are compiled elsewhere, so I think there may be a problem with this location. My IOAPI is version 3.2 and NetCDF is version 4.4 I tried to modify the makfile in the smoke/src/xxx file,
LIBS = (LDIRS) (LIBS_SYS) (LIBS_COMPILE) -L/home/yz/model_lib/netcdf/lib -lnetcdff -lnetcdf LIBS_DEBUG = (LDIRS) (LIBS_DEBUG_SYS) (LIBS_COMPILE) -L/home/yz/model_lib/netcdf/lib -lnetcdff -lnetcdf
FFLAGS = -O3 -132 -zero -save -common-args -convert big_endian
-I/home/yz/SMOKE3-5/SMOKE3-2018/subsys/ioapi_includes
-I/home/yz/model_lib/netcdf/include

But the problem still hasn’t been solved
I hope to get your help. Thank you.
output_error.txt (169.1 KB)

eyth.alison · November 21, 2024, 3:10pm

The latest version of SMOKE is 5.1. We aren’t supporting versions as old as 3.5 at this time.

cjcoats · November 21, 2024, 3:23pm

The problems start here, with include-paths:

ifort -O3 -132 -zero -save -common-args -convert big_endian -I/home/yz/SMOKE3-5/SMOKE3-2018/subsys/ioapi_includes -I/home/yz/model_lib/netcdf/include -c -o grwinven.o grwinven.f
grwinven.f(51): error #5102: Cannot open include file 'EMCNST3.EXT'
        INCLUDE 'EMCNST3.EXT'   !  emissions constant parameters
----------------^
grwinven.f(52): error #5102: Cannot open include file 'IODECL3.EXT'
        INCLUDE 'IODECL3.EXT'   !  I/O API function declarations
----------------^
grwinven.f(53): error #5102: Cannot open include file 'SETDECL.EXT'
        INCLUDE 'SETDECL.EXT'   !  FileSetAPI variables and functions
----------------^
grwinven.f(45): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [MODFILESET]
        USE MODFILESET

[etc…

The netCDF INCLUDEs are unnecessary.
The I/O API INCLUDEs should point to the fixed_src sub-directory of your I/ API installation: -I[something]/ioapi-3.2/ioapi/fixed_src.
You also need include-directives for the SMOKE INCLUDE-files and MODULE-files:
-I/home/yz/SMOKE-3.5/SMOKE3-2018/subsys/smoke/src//inc
and
-I/home/yz/SMOKE-3.5/SMOKE3-2018/subsys/smoke/src/emmod/Linux2_x86_64ifort

By the way, the name is not “IOAPI”; it is “I/O API”, which stands for “Input/Output Applications Programming Interface”.

– Carlie J. Coats, Jr., Ph.D.
I/O API author/manager

MMengxin · November 21, 2024, 3:34pm

Thank you very much for your answer. I feel ashamed of the incorrect naming of the I/O API. Thank you again for your efforts.

MMengxin · November 21, 2024, 3:35pm

Thank you for your suggestion

MMengxin · November 24, 2024, 12:36pm

Following your guidance and suggestions, I have modified the relevant makefile files in src to read as follows: LIBS=(LDIRS) (LIB_SYS) $(LIBS-COMPILE)
-L/home/yz/model_lib/netcdf/lib -lnetcdff -lnetcdf -qopenmp
-L/home/yz/model_lib/hdf5/lib -lhdf5_fortran -lhdf5_hl -lhdf5
-L/home/yz/model_lib/zlib -lz

LIBS_DEBUG = (LDIRS) (LIBS_DEBUG_SYS) $(LIBS_COMPILE)
-L/home/yz/model_lib/netcdf/lib -lnetcdff -lnetcdf
-L/home/yz/model_lib/hdf5/lib -lhdf5_hl -lhdf5
-L/home/yz/model_lib/zlib -lz

LIBS_PVM = (LDIRS) -liocpl (LIBS) -lpvm3 -mp (LIBS_COMPILE) LIBS_PVMDB = (LDIRS) -liocpl (LIBS) -lpvm3 -mp (LIBS_COMPILE)
FFLAGS = -O3 -132 -zero -save -common-args -convert big_endian
-I/home/yz/SMOKE-3.5/SMOKE3-2018/subsys/smoke/src/inc
-I/home/yz/SMOKE-3.5/SMOKE3-2018/subsys/smoke/src/emmod/Linux2_x86_64ifort
-I/home/yz/model_lib/ioapi-3.2/ioapi/fixed_src
-I/home/yz/SMOKE-3.5/SMOKE3-2018/subsys/edss_tools/src/modules/Linux2_x86_64ifort
-I/home/yz/SMOKE-3.5/SMOKE3-2018/subsys/filesetapi/Linux2_x86_64ifort
-I/home/yz/model_lib/hdf5/include
-I/home/yz/model_lib/zlib/include
-I/home/yz/model_lib/netcdf/include
Although the compilation was successful, by then I saw logs related to netcdf related issues

output_error.txt (528.3 KB)
Supplement on November 25, 2024: In Dr Under Coats’ guidance and advice, I identified the cause of the error. The makefile in the src/smkmmerge file had a definition for LIBS2, but I did not make any changes. Therefore, I later modified it to be the same as LIBS (LIBS2=(LDIRS) (LIB_SYS) $(LIBS-COMPILE))
-L/home/yz/model_lib/netcdf/lib -lnetcdff -lnetcdf
-L/home/yz/model_lib/hdf5/lib -lhdf5_fortran -lhdf5_hl -lhdf5
-L/home/yz/model_lib/zlib -lz）
Successfully compiled through the following steps:
source /home/yz/SMOKE-3.5/SMOKE3-2018/scripts/platform
cd /home/yz/SMOKE-3.5/SMOKE3-2018/subsys/smoke/assigns
source ASSIGNS.nctox.cmaq.cb05_soa.us12-nc
cd /home/yz/SMOKE-3.5/SMOKE3-2018/subsys/smoke/scripts/make

./Makeall clean

./Makeall >& output_error.txt

Thank you again, Dr Coats, your guidance

cjcoats · November 24, 2024, 12:47pm

With netCDF4 libraries, you need to build both the Fortran libnetcdff.a and the C libnetcdf.a

Then your library-flags needs -lnetcdff -lnetcdf

MMengxin · November 24, 2024, 1:25pm

Yes, I have

already built the NETCDF library

cjcoats · November 24, 2024, 1:30pm

You still need library-flags -lnetcdff -lnetcdf

MMengxin · November 24, 2024, 1:37pm

I may still not understand the specific location you mentioned. Could you please let me know if this setup works? Are you referring to this place.
LIBS = (LDIRS) (LIBS_SYS) $(LIBS_COMPILE)
-L/home/yz/model_lib/netcdf/lib -lnetcdff -lnetcdf -qopenmp
-L/home/yz/model_lib/hdf5/lib -lhdf5_fortran -lhdf5_hl -lhdf5
-L/home/yz/model_lib/zlib -lz -qopenmp

cjcoats · November 24, 2024, 1:41pm

Look at the first command in the second of your included screen-captures at the top…

MMengxin · November 24, 2024, 1:44pm

I was too careless and didn’t even notice this mistake. Thank you for reminding me.

MMengxin · December 30, 2024, 7:11am

This is my platform setup, which needs to be changed from the beginning. Please refer to the official documentation for the specific installation process。

setenv SMOKE_EXE Linux2_x86_64ifort

if ( $SMOKE_EXE == Linux2_x86_64pg ) then
setenv FC /nas02/apps/pgi-10.3/linux86-64/10.3/bin/pgf90
setenv FFLAG "-O2 -Msave -Mbackslash -Mbyteswapio -Kieee -Mextend -Bstatic "
setenv DBGFLAG “-g -Mbounds -Msave -Mbackslash -Mbyteswapio -Kieee -Mextend -Bstatic”
else if ( SMOKE_EXE == Linux2_x86_64ifort ) then setenv FC ifort setenv FFLAG "-O3 -132 -zero -save -common-args -convert big_endian" setenv DBGFLAG "-g -132 -zero -save -common-args -convert big_endian" else if ( ! ?FC || ! ?FFLAG || ! ?DBGFLAG ) then
echo “”
if ( ! ?FC ) echo "--> Compiler variable FC undefined..." if ( ! ?FFLAG ) echo “–> Compiler flag variable FFLAG undefined…”
if ( ! $?DBGFLAG ) echo “–> Compiler flag variable DBGFLAG undefined…”
echo “”
echo “–> Set the variables above to proceed…”
echo “”
exit( 1 )
endif
endif

exit( 0 )

eyth.alison · December 31, 2024, 4:09am

Please explain why you are using such an old version of SMOKE. We are not normally trying to support versions that are this old.

MMengxin · February 18, 2025, 10:25am

Thank you for your question. Hello, I am using this older version of SMOKE to learn how to configure different versions of SMOKE on a computer.

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SMOKE3.5 is based on Intel Ifort error reporting

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