[MITgcm-support] [EXTERNAL] Re: Compiling Problems
Madeleine Youngs
myoungs at umd.edu
Tue Aug 20 16:50:20 EDT 2024
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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