Errors compiling m3tools

I/O API m3tools
1

Trying to compile ioapi3.2 on cluster running two 64-core AMD Epyc “Milan” processors. Im using Intel compiler and admin. installed netCDF C and netCDF fortran also compiled with intel (and curl and MPI) with netCDF4. Following the CMAS install instructions I used DEFINEFLAGS = -DIOAPI_NCF4=1 (since netCDF4 was not disabled) and comment out OMPFLAGS = #-qopenmp, OMPLIBS = #-qopenmp in Makeinclude.Linux2_x86_64ifort.

ioapi looks to compile fine, but error chain pops up once m3tools starts to compile. I read and tried the fixes for the same problem to no avail. ChatGPT says the error are do to a linkage problem with netCDF, but all AI suggested fixes failed

Partial make.log when the trouble starts

make[1]: Leaving directory ‘/depot/gmichals/apps/Greg_CMAQ/ioapi-3.2/ioapi’
(cd /depot/gmichals/apps/Greg_CMAQ/ioapi-3.2/m3tools ; make BIN=Linux2_x86_64ifort all)
make[1]: Entering directory ‘/depot/gmichals/apps/Greg_CMAQ/ioapi-3.2/m3tools’
cd /depot/gmichals/apps/Greg_CMAQ/ioapi-3.2/Linux2_x86_64ifort; ifort -auto -warn notruncated_source /depot/gmichals/apps/Greg_CMAQ/ioapi-3.2/Linux2_x86_64ifort/airs2m3.o -L/depot/gmichals/apps/Greg_CMAQ/ioapi-3.2/Linux2_x86_64ifort -lioapi “nf-config --flibs nc-config --libs” -o airs2m3
/depot/gmichals/apps/Greg_CMAQ/ioapi-3.2/Linux2_x86_64ifort/libioapi.a(init3.o): In function init3_': init3.F90:(.text+0x6a): undefined reference to nf_inq_libvers_’
/depot/gmichals/apps/Greg_CMAQ/ioapi-3.2/Linux2_x86_64ifort/libioapi.a(open3.o): In function open3_': open3.F90:(.text+0xc01): undefined reference to nf_close_’
/depot/gmichals/apps/Greg_CMAQ/ioapi-3.2/Linux2_x86_64ifort/libioapi.a(opnfil3.o): In function opnfil3_': opnfil3.F90:(.text+0xb0): undefined reference to nf_open_’
opnfil3.F90:(.text+0xe9): undefined reference to nf_get_att_int_' opnfil3.F90:(.text+0x117): undefined reference to nf_get_att_int_’
opnfil3.F90:(.text+0x16a): undefined reference to nf_get_att_int_' opnfil3.F90:(.text+0x198): undefined reference to nf_get_att_int_’
opnfil3.F90:(.text+0x1c6): undefined reference to nf_get_att_int_' /depot/gmichals/apps/Greg_CMAQ/ioapi-3.2/Linux2_x86_64ifort/libioapi.a(opnfil3.o):opnfil3.F90:(.text+0x1f4): more undefined references to nf_get_att_int_’ follow

2

Are nf-config and nc-config in your PATH? (They need to be – or else do these commands “by hand” and put in the results here.).

And where did the double-quote come from? This needs to be a back-quote. Or else the result of this pair of commands

3

yes they are in my path. even tried explicit paths in the Makefile

include /depot/gmichals/apps/Greg_CMAQ/ioapi-3.2/ioapi/Makeinclude.${BIN}

Manually setting NetCDF paths and libraries

NETCDF_C_LIB_DIR = /apps/spack/negishi/apps/netcdf-c/4.9.0-intel-19.1.3-lnodl34/lib
NETCDF_FORTRAN_LIB_DIR = /apps/spack/negishi/apps/netcdf-fortran/4.6.0-intel-19.1.3-lxhp25h/lib
NETCDF_INCLUDE_DIR = /apps/spack/negishi/apps/netcdf-c/4.9.0-intel-19.1.3-lnodl34/include

Setting CURL library path

CURL_LIB_DIR = /apps/spack/negishi/apps/curl/7.85.0-gcc-8.5.0-xsntqgd/lib

Set environment variables

export CRAYPE_LINK_TYPE=static
export LIBRARY_PATH=$$LIBRARY_PATH:$(CURL_LIB_DIR)

Compiler flags

FFLAGS = -I$(IODIR) -I$(NETCDF_INCLUDE_DIR) {MODI} (OBJDIR) -DIOAPI_NCF4 (ARCHFLAGS) (PARFLAGS) (FOPTFLAGS) (ARCHFLAGS)
LDFLAGS = -I$(IODIR) (DEFINEFLAGS) (ARCHFLAGS)

Libraries to link

LIBS = -L${OBJDIR} -L$(NETCDF_C_LIB_DIR) -L$(NETCDF_FORTRAN_LIB_DIR) -lioapi -lnetcdff -lnetcdf -lm (OMPLIBS) (ARCHLIB) $(ARCHLIBS)

VPATH = ${OBJDIR}

4

So what does that entire line that generates the error look like ??

5

full make log
logfile.txt (39.7 KB)

6

I repeat: why those damned double-quotes ???

7

Found them in the ioapi3.2 Makefile not in m3tools Makefile looks to have been the problem! Thanks ive come to loathe the plethora of Makefiles, Makefile.seds over the past 3 days!