pbdNCDF4 with parallel I/O : installation fails on compilation of pncdf4.c

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Dave Biagioni

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Aug 14, 2014, 6:34:41 PM8/14/14

to rbigdatap...@googlegroups.com, Ryan Elmore

Hello--

I am trying to install pbdNCDF4 with parallel support, and am encountering the following error. I tried to trace back where the undeclared variables should be coming from, but without much success. As far as I can tell, the serial installation was successful, differing only in the absence of --enable-parallel in --configure-args. Both hdf5-1.3.11 and netcdf-4.3.3 built successfully and passed make check, including parallel i/o tests. I am happy to provide additional details, and any feedback would be much appreciated!

===============================================

[dbiagion@login4 src]$ R_LIBS=/nopt/nrel/apps/R/3.1.0-gcc/lib64/R/library/:/home/dbiagion/usr/local/R/ R --no-site-file CMD INSTALL --configure-args="--with-nc-config=/home/dbiagion/usr/local/netcdf-c/bin/nc-config --enable-parallel" --library=/home/dbiagion/usr/local/R/tmp pbdNCDF4_0.1-4.tar.gz

* installing *source* package ‘pbdNCDF4’ ...

** package ‘pbdNCDF4’ successfully unpacked and MD5 sums checked

user specified nc-config is /home/dbiagion/usr/local/netcdf-c/bin/nc-config

checking for nc-config... yes

Netcdf library version: netCDF 4.3.3-rc1

Netcdf library has version 4 interface present: yes

Netcdf library was compiled with C compiler: /nopt/nrel/apps/openmpi/1.7.3-serial-gcc-4.8.2/bin/mpicc

configure: creating ./config.status

config.status: creating src/Makevars

configure: creating ./config.status

config.status: creating src/Makevars

config.status: creating R/zzz.R

****************** Results of ncdf4 package configure *******************

SPMD_CPPFLAGS = -I/nopt/nrel/apps/openmpi/1.7.3-serial-gcc-4.8.2/include -DMPI2 -DOPENMPI

SPMD_LDFLAGS = -L/nopt/nrel/apps/openmpi/1.7.3-serial-gcc-4.8.2/lib -lmpi -lutil -lpthread

NETCDF_HEADER = /home/dbiagion/usr/local/netcdf-c/include/netcdf_par.h

NETCDF_INCLUDE = 1

NETCDF_PAR = TRUE

NETCDF_PAR_OBJS = pncdf4.o

netCDF v4 CPP flags = -I/home/dbiagion/usr/local/netcdf-c/include

netCDF v4 LD flags = -L/home/dbiagion/usr/local/netcdf-c/lib -lnetcdf -lhdf5 -lhdf5_hl -ldl -lm -lz -lcurl

netCDF v4 runtime path =

*************************************************************************

** libs

echo "SPMD_CPPFLAGS = -I/nopt/nrel/apps/openmpi/1.7.3-serial-gcc-4.8.2/include -DMPI2 -DOPENMPI" > Makeconf

echo "SPMD_LDFLAGS = -L/nopt/nrel/apps/openmpi/1.7.3-serial-gcc-4.8.2/lib -lmpi -lutil -lpthread" >> Makeconf

echo "NETCDF_HEADER = /home/dbiagion/usr/local/netcdf-c/include/netcdf_par.h" >> Makeconf

echo "NETCDF_INCLUDE = 1" >> Makeconf

echo "NETCDF_PAR = TRUE" >> Makeconf

echo "NETCDF_PAR_OBJS = pncdf4.o" >> Makeconf

echo "NETCDF_CPPFLAGS = -I/home/dbiagion/usr/local/netcdf-c/include -DNETCDF_INCLUDE=1" >> Makeconf

echo "NETCDF_LDFLAGS = -L/home/dbiagion/usr/local/netcdf-c/lib -lnetcdf -lhdf5 -lhdf5_hl -ldl -lm -lz -lcurl" >> Makeconf

echo "NETCDF_RPATH = " >> Makeconf

echo "HAVE_NETCDF = TRUE" >> Makeconf

echo "PKG_CPPFLAGS = -I/home/dbiagion/usr/local/netcdf-c/include -DNETCDF_INCLUDE=1 -I/nopt/nrel/apps/openmpi/1.7.3-serial-gcc-4.8.2/include -DMPI2 -DOPENMPI" >> Makeconf

echo "PKG_LIBS = -L/home/dbiagion/usr/local/netcdf-c/lib -lnetcdf -lhdf5 -lhdf5_hl -ldl -lm -lz -lcurl -L/nopt/nrel/apps/openmpi/1.7.3-serial-gcc-4.8.2/lib -lmpi -lutil -lpthread" >> Makeconf

gcc -std=gnu99 -I/nopt/nrel/apps/R/3.1.0-gcc/lib64/R/include -DNDEBUG -I/home/dbiagion/usr/local/netcdf-c/include -DNETCDF_INCLUDE=1 -I/nopt/nrel/apps/openmpi/1.7.3-serial-gcc-4.8.2/include -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -c ncdf2.c -o ncdf2.o

pncdf4.c: In function ‘R_nc4_open_par’:

pncdf4.c:30:13: error: ‘NC_NOWRITE’ undeclared (first use in this function)

nc_mode = NC_NOWRITE;

pncdf4.c:30:13: note: each undeclared identifier is reported only once for each function it appears in

pncdf4.c:32:27: error: ‘NC_WRITE’ undeclared (first use in this function)

nc_mode = NC_WRITE;

pncdf4.c:46:55: error: ‘NC_MPIIO’ undeclared (first use in this function)

*retval = nc_open_par(R_ExpandFileName(filename[0]), NC_MPIIO, nc_comm,

pncdf4.c:48:16: error: ‘NC_NOERR’ undeclared (first use in this function)

if(*retval != NC_NOERR){

pncdf4.c:49:3: warning: implicit declaration of function ‘nc_strerror’ [-Wimplicit-function-declaration]

Rprintf("Error in R_nc4_open_par: %s\n", nc_strerror(*retval));

pncdf4.c: In function ‘R_nc4_create_par’:

pncdf4.c:71:15: error: ‘NC_NOCLOBBER’ undeclared (first use in this function)

nc_cmode += NC_NOCLOBBER;

pncdf4.c:74:15: error: ‘NC_SHARE’ undeclared (first use in this function)

nc_cmode += NC_SHARE;

pncdf4.c:77:15: error: ‘NC_64BIT_OFFSET’ undeclared (first use in this function)

nc_cmode += NC_64BIT_OFFSET;

pncdf4.c:80:15: error: ‘NC_NETCDF4’ undeclared (first use in this function)

nc_cmode += NC_NETCDF4;

pncdf4.c:83:15: error: ‘NC_MPIIO’ undeclared (first use in this function)

nc_cmode += NC_MPIIO;

pncdf4.c:86:15: error: ‘NC_MPIPOSIX’ undeclared (first use in this function)

nc_cmode += NC_MPIPOSIX;

pncdf4.c:99:16: error: ‘NC_NOERR’ undeclared (first use in this function)

if(*retval != NC_NOERR){

pncdf4.c: In function ‘R_nc4_var_par_access’:

pncdf4.c:120:12: error: ‘NC_NOERR’ undeclared (first use in this function)

if(err != NC_NOERR){

make: *** [pncdf4.o] Error 1

ERROR: compilation failed for package ‘pbdNCDF4’

* removing ‘/home/dbiagion/usr/local/R/tmp/pbdNCDF4’

* restoring previous ‘/home/dbiagion/usr/local/R/tmp/pbdNCDF4’

Romain C

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Aug 18, 2015, 11:51:49 AM8/18/15

to RBigDataProgramming, rtel...@gmail.com

Hi Dave --

Any chance you solved this (old) issue ? I am facing it right now with no clue on how to fix it !

It seems that --configure-args='--enable-parallel' points to netcdf_par.h but "NC_WRITE - like" declarations are only set in netcdf.h...

Am I mistaken ?

Cheers

Romain C

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Aug 18, 2015, 1:17:21 PM8/18/15

to RBigDataProgramming, rtel...@gmail.com

Hi all --

I guess I found my issues. The dependencies were not correctly compiled. I started from scratch with pbdPROF, pbdMPI and finally pbdNCDF4 and this time it worked perfectly.