[MITgcm-support] [EXTERNAL] Re: Compiling Problems
Madeleine Youngs
myoungs at umd.edu
Tue Aug 20 17:55:55 EDT 2024
Hi Samar,
I have tried running it with your gfortran optfile that you sent along and have the same errors. Would it be helpful if I sent along the error code using those options? Does it work for cray with the options you sent?
Madeleine
> On Aug 20, 2024, at 2:50 PM, Samar Khatiwala <samar.khatiwala at earth.ox.ac.uk> wrote:
>
> Hi Madeleine,
>
> It doesn’t seem you're using a derecho-specific optfile when invoking genmake. Nor do you appear to be specifying the path to the MPI library.
>
> If I remember, on derecho the compiler wrappers mpif90 etc don’t automatically link to the MPI libraries. You need to explicitly specify the path in your optfile. You can find out what libraries/include paths are being used by doing 'mpif90 -v’ (or 'mpif90 -show' on sensible MPI installations which unfortunately cray isn’t).
>
> Samar
>
>> On Aug 20, 2024, at 9:50 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
>>>>> _______________________________________________
>>>>> MITgcm-support mailing list
>>>>> MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
>>>>> http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support <https://urldefense.us/v3/__http:/mailman.mitgcm.org/mailman/listinfo/mitgcm-support__;!!PvBDto6Hs4WbVuu7!NnRx5vlbDYZWIRraW2gZnWzzXsE782jeSZ_0N-DP52xAVkHbj-uEwC3rZ_U5PHL8Ay0r9294n_QD_GmOPdGy$>
>>>>>
>>>>> _______________________________________________
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>>>>> http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support <https://urldefense.us/v3/__http:/mailman.mitgcm.org/mailman/listinfo/mitgcm-support__;!!PvBDto6Hs4WbVuu7!NnRx5vlbDYZWIRraW2gZnWzzXsE782jeSZ_0N-DP52xAVkHbj-uEwC3rZ_U5PHL8Ay0r9294n_QD_GmOPdGy$>
>>>>>
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>>>>
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>>>
>>
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