Error During LIS Setup #849

rman500 · 2021-07-21T20:41:31Z

rman500
Jul 21, 2021

Hello,

I'm attempting to setup LIS on an Ubuntu20.04LTS system using gcc/gfortran7.3. I've gotten the prerequisites installed without issue. However, when attempting to compile after using the configure script I get this message:

/usr/bin/gfortran-7 -c -ffree-line-length-0 -O2 -fbacktrace -fconvert=big-endian -DHIDE_SHR_MSG -DNO_SHR_VMATH -DGFORTRAN -DLINUX -DHIDE_MPI -I/usr/local/LIS/esmf-ESMF_8_1_1/mod/modO/Linux.gfortran.64.mpiuni.default -I/usr/local/LIS/eccodes-2.22.1-Source/build/include/ -DLIS_JULES -I./ -I../core/ -I../params/gfrac/SPORTDaily/ -I../params/gfrac/VIIRSDaily/ -I../surfacemodels/land/vic.4.1.1/ -I../surfacemodels/land/vic.4.1.1/physics/ -I../surfacemodels/land/vic.4.1.2.l/ -I../surfacemodels/land/vic.4.1.2.l/physics/ -I../surfacemodels/land/awral.6.0.0/physics/ -I../surfacemodels/land/rdhm.3.5.6/ -I../surfacemodels/land/rdhm.3.5.6/sac/ -I../surfacemodels/land/rdhm.3.5.6/frz/ -I../surfacemodels/land/rdhm.3.5.6/snow17/ -I../surfacemodels/land/rdhm.3.5.6/sachtet/ ../core/LIS_domainMod.F90
../core/LIS_domainMod.F90:3176:39:

mode=NF90_NOWRITE,ncid=nid)
1
Error: Symbol ‘nf90_nowrite’ at (1) has no IMPLICIT type
../core/LIS_domainMod.F90:3569:28:

start=(/sc,sr/), &
1
Error: Keyword argument requires explicit interface for procedure ‘nf90_get_var’ at (1)
../core/LIS_domainMod.F90:3568:9:

ios = nf90_get_var(nid, landmaskid, array, &
1
Error: Function ‘nf90_get_var’ at (1) has no IMPLICIT type
../core/LIS_domainMod.F90:3191:12:

ios = nf90_inq_varid(nid,'LANDMASK',landmaskid)
1
Error: Function ‘nf90_inq_varid’ at (1) has no IMPLICIT type
../core/LIS_domainMod.F90:3344:12:

ios = nf90_close(nid)
1
Error: Function ‘nf90_close’ at (1) has no IMPLICIT type
make: *** [Makefile:140: LIS_domainMod.o] Error 1

[ERR] Compile failed

Does anyone know what I may be doing wrong?

Thanks!

Answered by dmocko

Mar 8, 2022

Hi @bmcandr - thanks for bringing up my earlier comment. Yes, the compiler libraries should be in the $LD_LIBRARY_PATH before prepending the LISF-required libraries.

@Benminoungou Please again copy the entire results of "echo $LD_LIBRARY_PATH" to confirm. There may have been a cut-and-paste error in your earlier response.

View full answer

dmocko · 2021-07-21T20:54:21Z

dmocko
Jul 21, 2021
Collaborator

Hi,

Can you please attach a copy of your configure.lis file (created during the "configure" step)?

This file can be found in LISF/lis/make.

It seems that you are not pointing to the netCDF libraries correctly.

David

14 replies

bmcandr Mar 8, 2022

Thanks. It looks like the NetCDF library may not be properly installed (edit: or netcdf/bin is not in your path). Do the executables nc-config and nf-config exist within /home/fanfar/local/lib/netcdf/bin?

Benminoungou Mar 8, 2022

Dear Brendan,
This is the content of : /home/fanfar/local/lib/netcdf/bin
(base) [fanfar@localhost lib]$ cd /home/fanfar/local/lib/netcdf/bin
(base) [fanfar@localhost bin]$ ls
nc-config nccopy ncdump ncgen ncgen3 nf-config

It's like nc-config and nf-config are there.

/Bernard

bmcandr Mar 8, 2022

Ok, good! Looks like this directory is just not on your path (I edited my previous comment to mention this possible caveat). Try running ./nc-config --all and ./nf-config --all from within that directory.

Benminoungou Mar 8, 2022

Dear Brendan,
Running ./nc-config --all or nc-config --all give different results as shown below:
(base) [fanfar@localhost ~]$ cd /home/fanfar/local/lib/netcdf/bin
(base) [fanfar@localhost bin]$ ./nc-config --all

This netCDF 4.6.3 has been built with the following features:

  --cc            -> gcc
  --cflags        -> -I/home/fanfar/local/lib/netcdf/include 
  --libs          -> -L/home/fanfar/local/lib/netcdf/lib -lnetcdf

  --has-c++       -> no
  --cxx           -> 

  --has-c++4      -> no
  --cxx4          -> 

  --has-fortran   -> yes
  --fc            -> gfortran
  --fflags        -> -I/usr/lib64/gfortran/modules
  --flibs         -> -lnetcdff
  --has-f90       -> 
  --has-f03       -> yes

  --has-dap       -> no
  --has-dap2      -> no
  --has-dap4      -> no
  --has-nc2       -> yes
  --has-nc4       -> no
  --has-hdf5      -> no
  --has-hdf4      -> no
  --has-logging   -> no
  --has-pnetcdf   -> no
  --has-szlib     -> 
  --has-cdf5      -> yes
  --has-parallel4 -> no
  --has-parallel  -> no

  --prefix        -> /home/fanfar/local/lib/netcdf
  --includedir    -> /home/fanfar/local/lib/netcdf/include
  --libdir        -> /home/fanfar/local/lib/netcdf/lib
  --version       -> netCDF 4.6.3

(base) [fanfar@localhost bin]$ nc-config --all

This netCDF 4.7.0 has been built with the following features:

  --cc            -> gcc
  --cflags        -> -I/usr/include -I/usr/include/hdf
  --libs          -> -L/usr/lib64 -lnetcdf
  --static        -> -ljpeg -lmfhdf -ldf -ljpeg -lsz -lhdf5_hl -lhdf5 -lm -ldl -lz -lcurl -ltirpc

  --has-c++       -> no
  --cxx           -> 

  --has-c++4      -> no
  --cxx4          -> 

  --has-fortran   -> yes
  --fc            -> gfortran
  --fflags        -> -I/usr/lib64/gfortran/modules
  --flibs         -> -lnetcdff
  --has-f90       -> 
  --has-f03       -> yes

  --has-dap       -> yes
  --has-dap2      -> yes
  --has-dap4      -> yes
  --has-nc2       -> yes
  --has-nc4       -> yes
  --has-hdf5      -> yes
  --has-hdf4      -> yes
  --has-logging   -> no
  --has-pnetcdf   -> no
  --has-szlib     -> yes
  --has-cdf5      -> yes
  --has-parallel4 -> no
  --has-parallel  -> no

  --prefix        -> /usr
  --includedir    -> /usr/include
  --libdir        -> /usr/lib64
  --version       -> netCDF 4.7.0

I don't know why.

/Bernard

bmcandr Mar 8, 2022

It looks like you have two different versions of the NetCDF C library that were built with different features and installed in different locations. I notice your shell prompt has (base) at the front--are you working within an Anaconda environment? If so, I recommend deactivating your conda environment before carefully building the required libraries from source and installing them into a custom prefix to ensure there are no conflicts.

For comparison, here is what the output of nc-config --all is in the GNU environment on our system:

This netCDF 4.8.1 has been built with the following features:

  --cc            -> /usr/local/other/gcc/11.2.0/bin/gcc
  --cflags        -> -I/discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/include -I/discover/nobackup/projects/lis/libs/sles-12.3/hdf5/1.12.1_gnu-11.2.0/include
  --libs          -> -L/discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/lib -lnetcdf
  --static        -> -lhdf5_hl -lhdf5 -lm -ldl -lz -lcurl

  --has-c++       -> no
  --cxx           ->

  --has-c++4      -> no
  --cxx4          ->

  --has-fortran   -> yes
  --fc            -> /usr/local/other/gcc/11.2.0/bin/gfortran
  --fflags        -> -I/discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/include -I/discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/include
  --flibs         -> -L/discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/lib -lnetcdff
  --has-f90       ->
  --has-f03       -> yes

  --has-dap       -> no
  --has-dap2      -> no
  --has-dap4      -> no
  --has-nc2       -> yes
  --has-nc4       -> yes
  --has-hdf5      -> yes
  --has-hdf4      -> no
  --has-logging   -> no
  --has-pnetcdf   -> no
  --has-szlib     -> no
  --has-cdf5      -> yes
  --has-parallel4 -> no
  --has-parallel  -> no
  --has-nczarr    -> yes

  --prefix        -> /discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0
  --includedir    -> /discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/include
  --libdir        -> /discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/lib
  --version       -> netCDF 4.8.1

And nf-config --all:

This netCDF-Fortran 4.5.3 has been built with the following features:

  --cc        -> /usr/local/other/gcc/11.2.0/bin/gcc
  --cflags    -> -I/discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/include -I/discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/include -DgFortran

  --fc        -> /usr/local/other/gcc/11.2.0/bin/gfortran
  --fflags    -> -I/discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/include -I/discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/include
  --flibs     -> -L/discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/lib -lnetcdff
  --has-f90   ->
  --has-f03   -> yes

  --has-nc2   -> yes
  --has-nc4   -> yes

  --prefix    -> /discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0
  --includedir-> /discover/nobackup/projects/lis/libs/sles-12.3/netcdf/4.8.1_gnu-11.2.0/include
  --version   -> netCDF-Fortran 4.5.3

@dmocko, do you have any other ideas? Returning to your earlier comment about $LD_LIBRARY_PATH, I notice that @Benminoungou's has a trailing : at the end that I'm guessing resulted from appending an empty $LD_LIBRARY_PATH to the end when exporting it in their .profile:

/home/fanfar/local/lib/esmf-ESMF_8_1_1/lib/libO/Linux.gfortran.64.mpiuni.default:/home/fanfar/local/lib/netcdf/lib:/usr/src/eccodes/lib:

Sounds like they should also add their compilers and standard libraries to $LD_LIBRARY_PATH before prepending it with the LISF required libraries? (OpenJPEG is also missing)

dmocko · 2022-03-08T21:18:49Z

dmocko
Mar 8, 2022
Collaborator

Hi @bmcandr - thanks for bringing up my earlier comment. Yes, the compiler libraries should be in the $LD_LIBRARY_PATH before prepending the LISF-required libraries.

@Benminoungou Please again copy the entire results of "echo $LD_LIBRARY_PATH" to confirm. There may have been a cut-and-paste error in your earlier response.

9 replies

dmocko Mar 21, 2022
Collaborator

Hi,

Once again, I am concerned about your LD_LIBRARY_PATH. It ends with a colon, and does not include any compiler directories.

In my LD_LIBRARY_PATH, I have all of the LIS-related libraries first, but then paths of several compiler directories, such as: "/usr/local/intel/oneapi/2021/compiler/2021.4.0/linux/lib".

In your .profile file, are you defining LD_LIBRARY_PATH in a similar way as shown here and in the LIS Users' Guide?

export LD_LIBRARY_PATH=$LIS_HDF5/lib:$LIS_LIBESMF:$LIS_NETCDF/lib:${LIS_ECCODES}/lib:$LD_LIBRARY_PATH

There are a couple other things I noticed:

You have "openjpen" in your LD_LIBRARY_PATH. Should this be "openjpeg"?
You may need to add "/lib" after "openjpeg".

David

Benminoungou Mar 21, 2022

Dear @dmocko,

I have changed LD_LIBRARY_PATH and it looks like:
echo $LD_LIBRARY_PATH
/home/fanfar/local/lib/compile/openjpeg/lib:/home/fanfar/local/lib/compile/esmf-ESMF_8_0_0/lib/libO/Linux.gfortran.64.mpiuni.default:/home/fanfar/local/lib/compile/netcdf/lib:/home/fanfar/local/lib/compile/eccodes/lib:/home/bernard/local/lib/hdf5/lib:/usr/bin

Compilers directories are: /usr/bin
I have also added this to .profile file:
export LD_LIBRARY_PATH=$LIS_HDF5/lib:$LIS_LIBESMF:$LIS_NETCDF/lib:${LIS_ECCODES}/lib:$LD_LIBRARY_PATH

The error remains. The error is similar to what a user had posted a few years earlier but unfortunately, no solution had been provided (https://sourceforge.net/p/mossco/tickets/89/). I suspect this is due to the lack of intelmpi.

Thank you for your support.

/Bernard

Benminoungou Mar 21, 2022

Dear @dmocko,
I have finally found the solution. In fact, in the configure.ldt or configure.lis it missing -lrt after -lesmf in LDFLAGS. I have just added it and it works now.
Thank you very much for your support.
Best regards,
/Bernard

dmocko Mar 21, 2022
Collaborator

Hi @Benminoungou,

Thanks so much for the update. Glad you were able to find a solution.

@jvgeiger and @bmcandr - I wonder if we should add the "-lrt" compiler option to arch/Config.pl for the linux_gfortran and the Darwin_gfortran system architecture options. This flag is present for all other system architectures.

bmcandr Mar 21, 2022

@dmocko I had the same idea, but I'll defer to Jim on this decision. Our current GNU 11.2.0 module sets $LIS_ARCH to linux_gfortran and works fine without -lrt so this may be operating system specific?

Now that I think about it, I believe I had to add this linker flag a while back when I was playing around with building a LIS Singularity container. I believe I was also trying to use CentOS as the base OS in the container...

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Error During LIS Setup #849

{{title}}

Replies: 2 comments 23 replies

{{title}}

{{title}}

{{editor}}'s edit

{{editor}}'s edit

{{title}}

{{title}}

{{title}}

{{editor}}'s edit

{{editor}}'s edit

{{title}}

{{editor}}'s edit

{{editor}}'s edit

{{title}}

{{title}}

{{editor}}'s edit

{{editor}}'s edit

{{title}}

{{title}}

{{title}}

{{title}}

{{editor}}'s edit

{{editor}}'s edit

Select a reply

Error During LIS Setup #849

Replies: 2 comments · 23 replies

dmocko Jul 21, 2021 Collaborator

dmocko Mar 8, 2022 Collaborator

dmocko Mar 21, 2022 Collaborator

dmocko Mar 21, 2022 Collaborator

Replies: 2 comments 23 replies

dmocko
Jul 21, 2021
Collaborator

dmocko
Mar 8, 2022
Collaborator

dmocko Mar 21, 2022
Collaborator

dmocko Mar 21, 2022
Collaborator