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wwieder / biogeochem_testbed

Soil biogeochemical testbed
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code won't compile #35

Closed wwieder closed 4 years ago

wwieder commented 4 years ago

Hi @melanniehartman I was hoping to try spinning up MIMICS-CN with new parameters, but couldn't get the source code to compile. Not sure if it's because of the compilers now available on CGD machines or something else? https://github.com/wwieder/biogeochem_testbed_1.1/blob/1e3e2d581ab8ccb97ffa19e87b0e286888933057/SOURCE_CODE/README.txt#L1

The error I'm getting is below:

corpse_variable.o corpse_soil_carbon.o corpse_inout.o corpse_cycle.o -L/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib -lnetcdff -lm /usr/bin/ld: warning: libgfortran.so.5, needed by /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so, not found (try using -rpath or -rpath-link) /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_reshape_4@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to_gfortran_runtime_error_at@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_shape_4@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to_gfortran_reshape_8@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_os_error@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to_gfortran_string_scan@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_size0@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to_gfortran_string_len_trim@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_internal_unpack@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to_gfortran_internal_pack@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to `_gfortran_concat_string@GFORTRAN_8' collect2: error: ld returned 1 exit status make: *** [casaclm_mimics-cn_corpse] Error 1

wwieder commented 4 years ago

found the right readme to load gnu compiler

melanniehartman commented 4 years ago

Yes, looks like something on the system changed. We might have to load a different module or use different paths in the Makefile. I'll check into it.

Melannie

On Thu, Sep 3, 2020 at 3:22 PM will wieder notifications@github.com wrote:

Hi @melanniehartman https://github.com/melanniehartman I was hoping to try spinning up MIMICS-CN with new parameters, but couldn't get the source code to compile. Not sure if it's because of the compilers now available on CGD machines or something else?

https://github.com/wwieder/biogeochem_testbed_1.1/blob/1e3e2d581ab8ccb97ffa19e87b0e286888933057/SOURCE_CODE/README.txt#L1

The error I'm getting is below:

corpse_variable.o corpse_soil_carbon.o corpse_inout.o corpse_cycle.o -L/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib -lnetcdff -lm /usr/bin/ld: warning: libgfortran.so.5, needed by /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so, not found (try using -rpath or -rpath-link) /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_reshape_4@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_runtime_error_at@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_shape_4@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_reshape_8@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_os_error@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_string_scan@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_size0@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_string_len_trim@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_internal_unpack@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_internal_pack@GFORTRAN_8' /usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to `_gfortran_concat_string@GFORTRAN_8' collect2: error: ld returned 1 exit status make: *** [casaclm_mimics-cn_corpse] Error 1

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wwieder commented 4 years ago

Don't worry. I figured it out

On Thu, Sep 3, 2020, 7:28 PM melanniehartman notifications@github.com wrote:

Yes, looks like something on the system changed. We might have to load a different module or use different paths in the Makefile. I'll check into it.

Melannie

On Thu, Sep 3, 2020 at 3:22 PM will wieder notifications@github.com wrote:

Hi @melanniehartman https://github.com/melanniehartman I was hoping to try spinning up MIMICS-CN with new parameters, but couldn't get the source code to compile. Not sure if it's because of the compilers now available on CGD machines or something else?

https://github.com/wwieder/biogeochem_testbed_1.1/blob/1e3e2d581ab8ccb97ffa19e87b0e286888933057/SOURCE_CODE/README.txt#L1

The error I'm getting is below:

corpse_variable.o corpse_soil_carbon.o corpse_inout.o corpse_cycle.o -L/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib -lnetcdff -lm /usr/bin/ld: warning: libgfortran.so.5, needed by

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so, not found (try using -rpath or -rpath-link)

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_reshape_4@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_runtime_error_at@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_shape_4@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_reshape_8@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_os_error@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_string_scan@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_size0@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_string_len_trim@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_internal_unpack@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to _gfortran_internal_pack@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so: undefined reference to `_gfortran_concat_string@GFORTRAN_8' collect2: error: ld returned 1 exit status make: *** [casaclm_mimics-cn_corpse] Error 1

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melanniehartman commented 4 years ago

Great! What was the problem?

On Thu, Sep 3, 2020 at 9:04 PM will wieder notifications@github.com wrote:

Don't worry. I figured it out

On Thu, Sep 3, 2020, 7:28 PM melanniehartman notifications@github.com wrote:

Yes, looks like something on the system changed. We might have to load a different module or use different paths in the Makefile. I'll check into it.

Melannie

On Thu, Sep 3, 2020 at 3:22 PM will wieder notifications@github.com wrote:

Hi @melanniehartman https://github.com/melanniehartman I was hoping to try spinning up MIMICS-CN with new parameters, but couldn't get the source code to compile. Not sure if it's because of the compilers now available on CGD machines or something else?

https://github.com/wwieder/biogeochem_testbed_1.1/blob/1e3e2d581ab8ccb97ffa19e87b0e286888933057/SOURCE_CODE/README.txt#L1

The error I'm getting is below:

corpse_variable.o corpse_soil_carbon.o corpse_inout.o corpse_cycle.o -L/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib -lnetcdff -lm /usr/bin/ld: warning: libgfortran.so.5, needed by

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so,

not found (try using -rpath or -rpath-link)

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_reshape_4@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_runtime_error_at@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_shape_4@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_reshape_8@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_os_error@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_string_scan@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_size0@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_string_len_trim@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_internal_unpack@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_internal_pack@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to `_gfortran_concat_string@GFORTRAN_8' collect2: error: ld returned 1 exit status make: *** [casaclm_mimics-cn_corpse] Error 1

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wwieder commented 4 years ago

I just forgot to load the right compiler... rookie move

module load compiler/gnu/8.1.0

On Fri, Sep 4, 2020 at 7:23 AM melanniehartman notifications@github.com wrote:

Great! What was the problem?

On Thu, Sep 3, 2020 at 9:04 PM will wieder notifications@github.com wrote:

Don't worry. I figured it out

On Thu, Sep 3, 2020, 7:28 PM melanniehartman notifications@github.com wrote:

Yes, looks like something on the system changed. We might have to load a different module or use different paths in the Makefile. I'll check into it.

Melannie

On Thu, Sep 3, 2020 at 3:22 PM will wieder notifications@github.com wrote:

Hi @melanniehartman https://github.com/melanniehartman I was hoping to try spinning up MIMICS-CN with new parameters, but couldn't get the source code to compile. Not sure if it's because of the compilers now available on CGD machines or something else?

https://github.com/wwieder/biogeochem_testbed_1.1/blob/1e3e2d581ab8ccb97ffa19e87b0e286888933057/SOURCE_CODE/README.txt#L1

The error I'm getting is below:

corpse_variable.o corpse_soil_carbon.o corpse_inout.o corpse_cycle.o -L/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib -lnetcdff -lm /usr/bin/ld: warning: libgfortran.so.5, needed by

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so,

not found (try using -rpath or -rpath-link)

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_reshape_4@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_runtime_error_at@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_shape_4@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_reshape_8@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_os_error@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_string_scan@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_size0@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_string_len_trim@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_internal_unpack@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to _gfortran_internal_pack@GFORTRAN_8'

/usr/local/netcdf-c-4.6.1-f-4.4.4-gcc-g++-gfortran-8.1.0/lib/libnetcdff.so:

undefined reference to `_gfortran_concat_string@GFORTRAN_8' collect2: error: ld returned 1 exit status make: *** [casaclm_mimics-cn_corpse] Error 1

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