[MITgcm-support] [EXTERNAL] Re: Compiling Problems

Jean-Michel Campin jmc at mit.edu
Wed Aug 14 18:02:51 EDT 2024


Hi,

Just to mentioned here the previous GitHub issue (just closed now) related to this subject:
 https://github.com/MITgcm/MITgcm/issues/853

Cheers,
Jean-Michel

On Wed, Aug 14, 2024 at 07:15:19PM +0000, Wang, Ou (US 329B) wrote:
> Yes, posting the *.f and *.F files as attachment is fine.
> 
> The other error/warning message related to running compiled test-program is due to not being able to find netCDF modules in your system. I think it is a different issue from the one not being able to generating diagnostics_ini_io.f.
> 
> Best,
> Ou
> 
> From: MITgcm-support <mitgcm-support-bounces at mitgcm.org> on behalf of Madeleine Youngs <myoungs at umd.edu>
> Date: Wednesday, August 14, 2024 at 11:53???AM
> To: mitgcm-support at mitgcm.org <mitgcm-support at mitgcm.org>
> Cc: dbonan at caltech.edu <dbonan at caltech.edu>
> Subject: Re: [MITgcm-support] [EXTERNAL] Re: Compiling Problems
> Hi All,
> 
> Thanks for all the support! I have tried the make CLEAN and the gfort compiler and I get the same error.  I do not have any code mods so it can???t be that.  I did successfully create diagnostics_check.f:
> 
> Would you want me to attach a file for the .f and .F files?
> 
> I also noticed this:
> original 'Makefile' generated but was unable to
>    run compiled test-program (please see 'genmake.log???)
> 
> 
> 
> 
> Thanks,
> Madeleine
> 
> 
> 
> running: check_fortran_compiler
> 
>  ftn -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -O2 -align -ip -c genmake_tcomp.f
> 
> ifort: command line warning #10121: overriding '-march=core-avx2' with '-march=core-avx2'
> 
>  ftn -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -O2 -align -ip -o genmake_tcomp genmake_tcomp.o
> 
> ifort: command line warning #10121: overriding '-march=core-avx2' with '-march=core-avx2'
> 
>  mpirun -np 1 ./genmake_tcomp
> 
> No host list provided
> 
>  --> set FC_CHECK= 3 /5
> 
> 
> 
> running: look_for_makedepend()
> 
>  --> set MAKEDEPEND=$(TOOLSDIR)/xmakedepend
> 
> 
> 
> running: check_HAVE_CLOC()
> 
>  running: get_fortran_c_namemangling()
> 
>  cc -O2 -ip -fPIC -c genmake_test.c
> 
> icc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
> 
> genmake_test.c(1): warning #266: function "tsub" declared implicitly
> 
>   void tcall( char * string ) { tsub( string ); }
> 
>                                 ^
> 
> 
> 
>  ftn -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -c genmake_tcomp.f
> 
> ifort: command line warning #10121: overriding '-march=core-avx2' with '-march=core-avx2'
> 
>  --> set FC_NAMEMANGLE='#define FC_NAMEMANGLE(X)  X ## _'
> 
> cc -O2 -ip -fPIC -c genmake_tc_1.c
> 
> icc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
> 
> ftn -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -o genmake_tc genmake_tc_2.f genmake_tc_1.o
> 
> ifort: command line warning #10121: overriding '-march=core-avx2' with '-march=core-avx2'
> 
>   HELLO WORLD   1723660750.37632
> 
>  --> set HAVE_CLOC='t'
> 
> 
> 
> running: check_HAVE_SETRLSTK()
> 
> cc -O2 -ip -fPIC -c genmake_tc_1.c
> 
> icc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
> 
>       program hello
> 
>       external setrlstk
> 
>       call setrlstk()
> 
>       end
> 
> ftn -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -o genmake_tc genmake_tc_2.f genmake_tc_1.o
> 
> ifort: command line warning #10121: overriding '-march=core-avx2' with '-march=core-avx2'
> 
>  --> set HAVE_SETRLSTK='t'
> 
> 
> 
> running: check_HAVE_SIGREG()
> 
> cc -O2 -ip -fPIC -c genmake_tc_1.c
> 
> icc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
> 
> genmake_tc_1.c(11): warning #274: declaration is not visible outside of function
> 
>       unsigned int sn, siginfo_t  si, struct ucontext *sc )
> 
>                                              ^
> 
> 
> 
>       program hello
> 
>       integer anint
> 
>       common /iv/ anint
> 
>       external sigreg
> 
>       call sigreg(anint)
> 
>       end
> 
> ftn -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -o genmake_tc genmake_tc_2.f genmake_tc_1.o
> 
> ifort: command line warning #10121: overriding '-march=core-avx2' with '-march=core-avx2'
> 
>  --> set HAVE_SIGREG='t'
> 
> 
> 
> running: check_HAVE_STAT()
> 
> cc -O2 -ip -fPIC -c genmake_tc_1.c
> 
>       program hello
> 
>       integer nbyte
> 
>       call tfsize(nbyte)
> 
>       print *," HELLO WORLD", nbyte
> 
>       end
> 
> ftn -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -o genmake_tc genmake_tc_2.f genmake_tc_1.o
> 
>  --> set HAVE_STAT='t'
> 
> 
> 
> running: check_netcdf_libs()
> 
> ===  genmake_tnc.F  >>>
> 
>       program fgennc
> 
> #include "netcdf.inc"
> 
>       integer iret, ncid, xid
> 
>       iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
> 
>       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
> 
>       iret = nf_def_dim(ncid, 'X', 11, xid)
> 
>       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
> 
>       iret = nf_close(ncid)
> 
>       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
> 
>       end
> 
> <<<  genmake_tnc.F  ===
> 
> 
> 
> cat genmake_tnc.F |  cpp -P -traditional -DALLOW_USE_MPI -DALWAYS_USE_MPI -DWORDLENGTH=4 -DNML_TERMINATOR -DALLOW_USE_MPI -DHAVE_SYSTEM -DHAVE_FDATE -DHAVE_ETIME_FCT -DHAVE_CLOC -DHAVE_SETRLSTK -DHAVE_SIGREG -DHAVE_STAT -I/opt/cray/pe/mpich/8.1.25/ofi/intel/19.0/include/
> 
>   WARNING: CPP failed to pre-process the netcdf test.
> 
>     Please check that $INCLUDES is properly set.
> 
> ftn   -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -O2 -align -ip -c genmake_tnc.f  \
> 
>   &&  ftn   -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -O2 -align -ip -o genmake_tnc.o
> 
> ifort: command line warning #10121: overriding '-march=core-avx2' with '-march=core-avx2'
> 
> genmake_tnc.f(12): error #5082: Syntax error, found END-OF-FILE when expecting one of: <LABEL> <END-OF-STATEMENT> ; <IDENTIFIER> TYPE MODULE ELEMENTAL IMPURE NON_RECURSIVE ...
> 
>       program fgennc
> 
> --------------------^
> 
> compilation aborted for genmake_tnc.f (code 1)
> 
> 
> 
> ==> try again with added '-lnetcdf'
> 
> cat genmake_tnc.F |  cpp -P -traditional -DALLOW_USE_MPI -DALWAYS_USE_MPI -DWORDLENGTH=4 -DNML_TERMINATOR -DALLOW_USE_MPI -DHAVE_SYSTEM -DHAVE_FDATE -DHAVE_ETIME_FCT -DHAVE_CLOC -DHAVE_SETRLSTK -DHAVE_SIGREG -DHAVE_STAT -I/opt/cray/pe/mpich/8.1.25/ofi/intel/19.0/include/ > genmake_tnc.f \
> 
>  &&  ftn   -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -O2 -align -ip -c genmake_tnc.f \
> 
>  &&  ftn   -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -O2 -align -ip -o genmake_tnc genmake_tnc.o  -lnetcdf
> 
> 
> 
> ==> try again with added '-lnetcdff -lnetcdf'
> 
> cat genmake_tnc.F |  cpp -P -traditional -DALLOW_USE_MPI -DALWAYS_USE_MPI -DWORDLENGTH=4 -DNML_TERMINATOR -DALLOW_USE_MPI -DHAVE_SYSTEM -DHAVE_FDATE -DHAVE_ETIME_FCT -DHAVE_CLOC -DHAVE_SETRLSTK -DHAVE_SIGREG -DHAVE_STAT -I/opt/cray/pe/mpich/8.1.25/ofi/intel/19.0/include/ > genmake_tnc.f \
> 
>  &&  ftn   -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -O2 -align -ip -c genmake_tnc.f \
> 
>  &&  ftn   -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g -O2 -align -ip -o genmake_tnc genmake_tnc.o  -lnetcdf
> 
>  --> set HAVE_NETCDF=''
> 
> 
> 
> running: check_HAVE_FLUSH()
> 
>   check_HAVE_FLUSH: successful
> 
>  --> set HAVE_FLUSH='t'
> 
> 
> 
> 
> 
> 
> 
> 
> On Aug 14, 2024, at 10:14 AM, Jody Klymak <jklymak at uvic.ca> wrote:
> 
> Hi Madeleine
> 
> When I have linking problems like this I sometimes fine `make CLEAN` to be a useful step if I???m not starting from a clean install.
> 
> Just a shot in the dark.
> 
> Cheers,  Jody
> 
> 
> On Aug 14, 2024, at 10:05???AM, Wang, Ou (US 329B) <ou.wang at jpl.nasa.gov> wrote:
> 
> You don't often get email from ou.wang at jpl.nasa.gov<mailto:ou.wang at jpl.nasa.gov>. Learn why this is important<https://urldefense.us/v3/__https:/aka.ms/LearnAboutSenderIdentification__;!!PvBDto6Hs4WbVuu7!KH725TbBJEI7MIlJLpQnN8eabPKjmhpEKwq5HuR2jxv1PbPahLcKS_MxXIyPkryZqzO8-g3zNi7bE8zw82RS$>
> Hi Madeleine,
> 
> Can you share your version of diagnostics_ini_io.f and diagnostics_ini_io.F? I would think the error is related to a broken link to ???DIAGNOSTICS.h???, not something related to the opt file. Also, did the compilation successfully generate diagnostics_check.f, which uses the variable ???diagMdsDir??? as well?
> It would be helpful if you can also share your versions of diagnostics_check.f and diagnostics_check.F.
> 
> Best,
> Ou Wang
> 
> 
> From: MITgcm-support <mitgcm-support-bounces at mitgcm.org<mailto:mitgcm-support-bounces at mitgcm.org>> on behalf of Madeleine Youngs <myoungs at umd.edu<mailto:myoungs at umd.edu>>
> Date: Tuesday, August 13, 2024 at 8:08???PM
> To: mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org> <mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>>
> Subject: [EXTERNAL] Re: [MITgcm-support] Compiling Problems
> Hi Takaya,
> 
> That didn???t seem to fix the issue, but thank you for sending this along!
> 
> Madeleine
> 
> On Aug 13, 2024, at 6:10 PM, Takaya Uchida <tu22 at fsu.edu<mailto:tu22 at fsu.edu>> wrote:
> 
> Hi Madeleine,
> 
> I???ve copy and pasted below the opt file I ended up using to compile MITgcm on Derecho.
> 
> #
> # Build options for Derecho at NCAR
> #
> 
> FC=ftn
> CC=cc
> DEFINES='-DALLOW_USE_MPI -DALWAYS_USE_MPI -DWORDLENGTH=4 -DNML_TERMINATOR'
> CPP='cpp -P -traditional'
> EXTENDED_SRC_FLAG='-132'
> NOOPTFLAGS='-O2 -g -march=core-avx2'
> LIBS=''
> INCLUDES='-I/opt/cray/pe/mpich/8.1.25/ofi/intel/19.0/include/'
> 
> if test "x$DEVEL" != x ; then
>     FFLAGS="$FFLAGS  -W0 -WB -convert big_endian -assume byterecl -fPIC -O0 -g -noalign -fpstkchk -check all -fpe0 -traceback -ftrapuv -fpmodel except -warn all -march=core-avx2"
> else
>     FFLAGS="$FFLAGS  -W0 -WB -convert big_endian -assume byterecl -fPIC -march=core-avx2 -g"
> fi
> 
> if test "x$IEEE" = x ; then
>         FOPTIM='-O2 -align -ip'
>         else
>         FOPTIM='-O2 -align -ip -mp'
> fi
> CFLAGS='-O2 -ip -fPIC'
> 
> The list of modules I load are:
> 
> module load ncarenv/23.09 craype/2.7.23 intel-classic/2023.2.1 ncarcompilers/1.0.0 cray-mpich/8.1.27 hdf5/1.12.2 netcdf/4.9.2
> 
> ----------------------------------
> Takaya Uchida (????????????)
> Assistant Research Scientist
> Florida State University
> Center for Ocean-Atmospheric Prediction Studies
> https://roxyboy.github.io/<https://urldefense.us/v3/__https:/roxyboy.github.io/__;!!PvBDto6Hs4WbVuu7!NnRx5vlbDYZWIRraW2gZnWzzXsE782jeSZ_0N-DP52xAVkHbj-uEwC3rZ_U5PHL8Ay0r9294n_QD_ImbsRJV$>
> 
> <Center for Ocean-Atmospheric Prediction Studies signature alt.png>
> 
> On Aug 13, 2024, at 8:51???PM, Madeleine Youngs <myoungs at umd.edu<mailto:myoungs at umd.edu>> wrote:
> 
> Hi Everyone,
> 
> I am working on compiling checkpoint68y on Derecho using no opt file (?) and I am getting this error.  Any advice on what the issue is?
> 
> 
> mpif90 -W0 -WB -msse2 -convert big_endian -assume byterecl -O2 -align -lmpich -lnetcdff -lnetcdf  -c diagnostics_fract_fill.f
> cat diagnostics_ini_io.F |  cpp  -traditional -P -DALLOW_USE_MPI -DALWAYS_USE_MPI -DWORDLENGTH=4 -DALLOW_USE_MPI -DHAVE_SYSTEM -DHAVE_FDATE -DHAVE_ETIME_FCT -DHAVE_CLOC -DHAVE_SETRLSTK -DHAVE_SIGREG -DHAVE_STAT -DHAVE_FLUSH  -I.  | ../../../tools/set64bitConst.sh  > diagnostics_ini_io.f
> mpif90 -W0 -WB -msse2 -convert big_endian -assume byterecl -O2 -align -lmpich -lnetcdff -lnetcdf  -c diagnostics_ini_io.f
> Cannot disable Fortran error message 6404
> diagnostics_ini_io.f(2005): error #6404: This name does not have a type, and must have an explicit type.   [DIAGMDSDIR]
>       IF ( diag_mdsio .AND. (diagMdsDir.NE.' ') .AND.
> -----------------------------^
> Cannot disable Fortran error message 6404
> diagnostics_ini_io.f(2006): error #6404: This name does not have a type, and must have an explicit type.   [DIAGMDSDIRCREATE]
>      &     diagMdsDirCreate .AND. (mdsioLocalDir.EQ.' ') ) THEN
> -----------^
> Cannot disable Fortran error message 6514
> diagnostics_ini_io.f(2009): error #6514: Substring or array slice notation requires CHARACTER type or array.   [DIAGMDSDIR]
>         WRITE(namBuf,'(3A)') ' mkdir -p ', diagMdsDir(1:iL), ' '
> -------------------------------------------^
> compilation aborted for diagnostics_ini_io.f (code 1)
> make[1]: *** [Makefile:1776: diagnostics_ini_io.o] Error 1
> make[1]: Leaving directory '/glade/derecho/scratch/myoungs/MITgcm/MultiWidthExperiments/Present9.20.16/build'
> make: *** [Makefile:1688: fwd_exe_target] Error 2
> 
> 
> Thanks,
> Madeleine
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