[MITgcm-support] Compiling problem by ifort: undefined reference to '_gfortran_st_write'

H.W. Shu shawn_chou at ees.hokudai.ac.jp
Wed Feb 10 04:42:00 EST 2021


Dear Dr. Martin,

Thank you for your message. 
In fact, I think I have the problem that I don't really know how to 
connect all these libraries into my compiling process. 
For example, 
I can load my netcdf library by : module load netcdf-fortran/4.5.2_intel
I also know my MPI directory: /opt/hpe/hpc/mpt/mpt-2.21/lib
so, in compiling process, I follow by the commands in "build" file as 
below:
$ module load netcdf-fortran/4.5.2_intel
$ ../../../tools/genmake2 -mods=../code  -mpi -of=/home/my_name/MITgcm_
c66j/tools/build_options/linux_amd64_ifort+mpi_ice_nas
$ make depend
$ make

note that I inserted the -mpi as you recommanded in previous mail in the 
command and also change my option file to linux_amd64_ifort+mpi_ice_nas
However, although at this moment I don't have the gfortran's problem
it gave me the other error message that:
-----
 -L/nasa/sgi/mpt/2.14r19/lib -lmpi -L/nasa/netcdf/4.0/lib -lnetcdf
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: 
main.o: in function `main':
main.f:(.text.startup+0x0): multiple definition of `main'; /opt/intel/
compilers_and_libraries_2020.0.166/linux/compiler/lib/intel64_lin/for_
main.o:for_main.c:(.text+0x0): first defined here
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: 
cannot find -lnetcdf
make[1]: *** [Makefile:1943: mitgcmuv] Error 1
make[1]: Leaving directory '/home/shawn_chou/MITgcm_c66j/verification/
totten_high/build'
make: *** [Makefile:1939: fwd_exe_target] Error 2
------

I have no further idea what is wrong at this moment.
I will really appreciate that if can have any hints. 

Thank you really much!

------
Dear Dr. Gus Correa

Thank you really much! 
After changing to other option-file, I dont have the gfortran's problem. 
but there's other one occurred as I described above. 

I will really appreciate if having any hints on this problem..
Thank you in advanced!

Best regards,
Shawn (Shu)




> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 09 Feb 2021 15:49:49 +0900
> From: "H.W. Shu" <shawn_chou at ees.hokudai.ac.jp>
> To: <mitgcm-support at mitgcm.org>
> Subject: [MITgcm-support] Compiling problem by ifort: undefined
> 	reference to	'_gfortran_st_write'
> Message-ID:
> 	<20210209064949.0032A501.0222 at HINES-WebMail.hines.hokudai.ac.jp>
> Content-Type: text/plain; charset=US-ASCII
> 
> Dear MITgcm users, 
> 
> Hello, this is Shawn from Hokkaido University.
> We are trying compiling an mpi run in our system by default compiler 
in 
> tools/build_options: linux_amd64_ifort
> (we added "-lmpi -03" in flags.)
> 
> However, in the process of Make,
> it told us that "undefined reference to '_gfortran_st_write_done'" and 
" 
> undefined reference to '_gfortran_transfer'".
> and leaved by this error. 
> 
> I am not familiar with compile problems, 
> I will really appreciate if can get any hint to start to fix the 
problem.
> 
> Thank you really much,
> 
> Best regards,
> Shawn
> 
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 9 Feb 2021 08:14:25 +0100
> From: Martin Losch <Martin.Losch at awi.de>
> To: MITgcm Support <mitgcm-support at mitgcm.org>
> Subject: Re: [MITgcm-support] Compiling problem by ifort: undefined
> 	reference to '_gfortran_st_write'
> Message-ID: <875C3E06-7FC8-456C-B4AD-B1657151B5D0 at awi.de>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Shawn,
> 
> normally you don?t have to add ?-lmpi" to the build options file. For 
MPI simulations it?s important that you add the -mpi flag to genmake2 
and that you know where your mpi include files are.
> Before you run genmake2 set the enviroment flag MPI_INC_DIR to the 
location of your mpifiles. E.g. on my laptop I installed OpenMP and have 
this:
> 
> >> echo $MPI_INC_DIR
> /opt/local/include/openmpi-mp
> >> ls /opt/local/include/openmpi-mp
> mpi-ext.h               mpi_portable_platform.h mpif-config.h          
 mpif-ext.h              mpif-handles.h          mpif-io-handles.h       
mpif-sizeof.h           openmpi
> mpi.h                   mpif-c-constants-decl.h mpif-constants.h       
 mpif-externals.h        mpif-io-constants.h     mpif-sentinels.h        
mpif.h
> 
> it?s important that ?mpif.h? is also in that directory.
> 
> Martin
> 
> 
> > On 9. Feb 2021, at 07:49, H.W. Shu <shawn_chou at ees.hokudai.ac.jp> 
wrote:
> > 
> > Dear MITgcm users, 
> > 
> > Hello, this is Shawn from Hokkaido University.
> > We are trying compiling an mpi run in our system by default compiler 
in 
> > tools/build_options: linux_amd64_ifort
> > (we added "-lmpi -03" in flags.)
> > 
> > However, in the process of Make,
> > it told us that "undefined reference to '_gfortran_st_write_done'" 
and " 
> > undefined reference to '_gfortran_transfer'".
> > and leaved by this error. 
> > 
> > I am not familiar with compile problems, 
> > I will really appreciate if can get any hint to start to fix the 
problem.
> > 
> > Thank you really much,
> > 
> > Best regards,
> > Shawn
> > 
> > 
> > _______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support
> 
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> 
> ------------------------------
> 
> Message: 3
> Date: Tue, 9 Feb 2021 02:14:08 -0500
> From: Gus Correa <gus at ldeo.columbia.edu>
> To: MITgcm Support <mitgcm-support at mitgcm.org>
> Subject: Re: [MITgcm-support] Compiling problem by ifort: undefined
> 	reference to '_gfortran_st_write'
> Message-ID:
> 	<CA+TEG=W3fPFcYnFv1bcPzeP12qGRy254xNZbSbVkD32r35HE8Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi H. W. Shu
> 
> Those are gfortran symbols that the Intel (ifort) compiler is unable 
to
> find,
> most likely when trying to link a library to the main MITgcm code.
> 
> If your MPI and netCDF libraries were compiled with gfortran,
> or, which is more common, if you installed them from packages in your 
Linux
> distribution,
> which normally compiles them with gfortran, it may be easier to try to 
use
> a build_options file that uses gfortran instead of Intel ifort.
> This is probably the shortest path to solve the problem.
> 
> If you prefer to use ifort, then a more laborious alternative is to 
compile
> MPI and netCDF
> from scratch (i.e., download the MPI and netCDF source code and 
compile)
> with Intel icc and ifort, and use them to link the MITgcm.
> 
> I hope this helps,
> 
> Gus Correa
> 
> On Tue, Feb 9, 2021 at 1:50 AM H.W. Shu <shawn_chou at ees.hokudai.ac.jp>
> wrote:
> 
> > Dear MITgcm users,
> >
> > Hello, this is Shawn from Hokkaido University.
> > We are trying compiling an mpi run in our system by default compiler 
in
> > tools/build_options: linux_amd64_ifort
> > (we added "-lmpi -03" in flags.)
> >
> > However, in the process of Make,
> > it told us that "undefined reference to '_gfortran_st_write_done'" 
and "
> > undefined reference to '_gfortran_transfer'".
> > and leaved by this error.
> >
> > I am not familiar with compile problems,
> > I will really appreciate if can get any hint to start to fix the 
problem.
> >
> > Thank you really much,
> >
> > Best regards,
> > Shawn
> >
> >
> > _______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support
> >
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