[R] R2.2.1-patched build failed with PGI 6.1 on x86-64

[Liaw, Andy]

Hi All,

While attempting to build R-patched using the Portland Group compiler suite
on our dual Opteron 250 box running Scyld 29cz5 (based on RH, kernel
2.4.29), I get:

make[5]: Leaving directory
`/home/andy/Rbuild/R221-pgi/src/library/tools/src'
make[5]: Entering directory
`/home/andy/Rbuild/R221-pgi/src/library/tools/src'
pgcc -I../../../../include  -I/include -I/include/CC   -fpic  -O2 -Kieee -c
/home/andy/Rbuild/R-patched/src/library/tools/src/text.c -o text.o
pgcc -I../../../../include  -I/include -I/include/CC   -fpic  -O2 -Kieee -c
/home/andy/Rbuild/R-patched/src/library/tools/src/init.c -o init.o
pgcc -I../../../../include  -I/include -I/include/CC   -fpic  -O2 -Kieee -c
/home/andy/Rbuild/R-patched/src/library/tools/src/Rmd5.c -o Rmd5.o
pgcc -I../../../../include  -I/include -I/include/CC   -fpic  -O2 -Kieee -c
/home/andy/Rbuild/R-patched/src/library/tools/src/md5.c -o md5.o
pgcc -shared  -L/libso -L/usr/lib64 -o tools.so text.o init.o Rmd5.o md5.o

mkdir -p -- ../../../../library/tools/libs
make[5]: Leaving directory
`/home/andy/Rbuild/R221-pgi/src/library/tools/src'
make[4]: Leaving directory
`/home/andy/Rbuild/R221-pgi/src/library/tools/src'
**ERROR: in routine alloca() there is a
stack overflow: thread 0, max 8180KB, used 0KB, request 16B
make[3]: *** [all] Error 1
make[3]: Leaving directory `/home/andy/Rbuild/R221-pgi/src/library/tools'
make[2]: *** [R] Error 1
make[2]: Leaving directory `/home/andy/Rbuild/R221-pgi/src/library'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/home/andy/Rbuild/R221-pgi/src'
make: *** [R] Error 1

I configured it as follows:

~/Rbuild/R-patched/configure \
     PG_HOME=/usr/pgi/linux86-64/6.1 \
     CC=pgcc \
     CFLAGS="-O2 -Kieee" \
     CPPFLAGS="-I$PG_HOME/include -I$PG_HOME/include/CC" \
     CPICFLAGS=-fpic \
     F77=pgf77 \
     FFLAGS="-Kieee"\
     FPICFLAGS=-fpic \
     CXX=pgCC \
     CXXFLAGS="-Kieee"\
     CXXPICFLAGS=-fpic \
     SHLIB_CXXLDFLAGS=-shared \
     SHLIB_LDFLAGS=-shared \
     LDFLAGS="-L$PG_HOME/libso -L/usr/lib64" \
     --with-blas="-L/usr/pgi/linux86-64/6.1/libso -lacml"

(Note that pgcc no longer recognize -mieee-fp, so I changed to -Kieee
instead, and had to manually remove -mieee-fp in the resulting Makeconf and
config.status.)

I'd very much appreciate any pointer as to how to proceed...

Best,
Andy


Andy Liaw, PhD
Biometrics Research    PO Box 2000 RY33-300
Merck Research Labs        Rahway, NJ 07065
andy_liaw(a)merck.com          732-594-0820