[MITgcm-support] [EXTERNAL] Re: Compiling Problems
Madeleine Youngs
myoungs at umd.edu
Tue Aug 20 16:58:04 EDT 2024
Here are the files requested.

> On Aug 20, 2024, at 1:50 PM, Madeleine Youngs <myoungs at umd.edu> wrote:
>
> Hi All,
>
> I have done some digging on my own. I ran testreport, which seemed to work fine with a single processor, but seems to be having similar issues for building with MPI. I thought to do this so it wasn’t dependent on my particular experiement. For example:
>
> Experiment: adjustment.128x64x1
>
> genmake ... successful
> clean build-dir: make Clean ...
> successful
> make depend ...
> successful
> make ...
> all_proc_die.f(789): error #5082: Syntax error, found END-OF-FILE when expecting one of: <LABEL> <END-OF-STATEMENT> ; <IDENTIFIER> TYPE MODULE ELEMENTAL IMPURE NON_RECURSIVE ...
> C-- Include MPI standard Fortran header file
> ----------------------------------------------^
> all_proc_die.f(270): error #6404: This name does not have a type, and must have an explicit type. [MYTHARG]
> SUBROUTINE ALL_PROC_DIE( myThArg )
> -------------------------------^
> compilation aborted for all_proc_die.f (code 1)
> make[1]: *** [Makefile:1223: all_proc_die.o] Error 1
> make[1]: Leaving directory '/glade/derecho/scratch/myoungs/MITgcm/verification/adjustment.128x64x1/build'
> make: *** [Makefile:1135: fwd_exe_target] Error 2
> failed
>
>
>> On Aug 14, 2024, at 11:51 AM, Madeleine Youngs <myoungs at umd.edu> wrote:
>>
>> 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://aka.ms/LearnAboutSenderIdentification>
>>>> 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$IEEE" = x ; then
>>>> FOPTIM='-O2 -align -ip'
>>>> else
>>>> FOPTIM='-O2 -align -ip -mp'
>>>> fi
>>>> CFLAGS='-O2 -ip -fPIC'
>>>>
>>>> The list of modules I load are:
>>>>
>>>> module load ncarenv/23.09 craype/2.7.23 intel-classic/2023.2.1 ncarcompilers/1.0.0 cray-mpich/8.1.27 hdf5/1.12.2 netcdf/4.9.2
>>>>
>>>> ----------------------------------
>>>> Takaya Uchida (内田貴也)
>>>> Assistant Research Scientist
>>>> Florida State University
>>>> Center for Ocean-Atmospheric Prediction Studies
>>>> https://roxyboy.github.io/ <https://urldefense.us/v3/__https:/roxyboy.github.io/__;!!PvBDto6Hs4WbVuu7!NnRx5vlbDYZWIRraW2gZnWzzXsE782jeSZ_0N-DP52xAVkHbj-uEwC3rZ_U5PHL8Ay0r9294n_QD_ImbsRJV$>
>>>>
>>>> <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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>>>>
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>>>>
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>
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