RichardsTJ2 at UPMC.EDU
2008-Aug-07 09:35 UTC
[Rd] config.log told me to report these (PR#12035)
Hello r-bugs, I am running openSuse 11.0, with my new Intel 8500 (Penryn) C2D, and I want to use icc and ifort. I was able to get a working Goto BLAS, following Dr. Goto's instructions. That seems to work OK with gcc and gfortran. I get about 10% faster computations by using -O3 rather than -O2. I get faster results with Goto BLAS rather than the R BLAS. Now I want to make icc and ifort work... So I tried this: ./configure CC=icc CFLAGS='-O3 -mp' CPPFLAGS=-I/opt/intel/cce/10.1.015/include/ F77=ifort CXX=icc CXXFLAGS='-O3 -mp' FFLAGS='-C90 -w90 -w95 -mp' CPICFLAGS=-shared CXXPICFLAGS=-shared FPICFLAGS=-shared SHLIB_LDFLAGS=-shared SHLIB_CXXLDFLAGS=-shared --with-blas="-L/usr/lib64/GotoBLAS -lgoto_penrynp-r1.26 -lpthread" I get six purported "bugs" in the config.log file (attached), but I hope there is something I've overlooked in the past week of agony. I have had similar log files with about 100 different combinations of options. I hope that you can help. Thank you so much. Tom Richards
Prof Brian Ripley
2008-Aug-09 06:04 UTC
[Rd] config.log told me to report these (PR#12035)
This looks like a thoroughly screwed-up compilation system, not an R problem. E.g. /usr/include/limits.h(125): error #5: could not open source file "limits.h" configure:5465: icc -E -traditional-cpp -I/opt/intel/cce/10.1.015/include/ conftest.c <command-line>:11: warning: "__GNUC_PATCHLEVEL__" redefined <built-in>:3: warning: this is the location of the previous definition In file included from /usr/include/features.h:331, from /usr/include/assert.h:38, from conftest.c:20: /usr/include/sys/cdefs.h:32: error: #error "You need a ISO C conforming compiler to use the glibc headers" /usr/include/limits.h(125): catastrophic error: could not open source file "limits.h" conftest.c(74): catastrophic error: could not open source file "dl.h" conftest.c(77): catastrophic error: could not open source file "floatingpoint.h" ./conftest: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory On Thu, 7 Aug 2008, RichardsTJ2 at UPMC.EDU wrote:> This is a multi-part message in MIME format. > > ------_=_NextPart_001_01C8EAD7.27542985 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > Hello r-bugs, > > I am running openSuse 11.0, with my new Intel 8500 (Penryn) C2D, and I > want to use icc and ifort. > I was able to get a working Goto BLAS, following Dr. Goto's > instructions. > That seems to work OK with gcc and gfortran. > I get about 10% faster computations by using -O3 rather than -O2. > I get faster results with Goto BLAS rather than the R BLAS. > Now I want to make icc and ifort work... > > So I tried this: > > ./configure CC=3Dicc CFLAGS=3D'-O3 -mp' > CPPFLAGS=3D-I/opt/intel/cce/10.1.015/include/ F77=3Difort CXX=3Dicc > CXXFLAGS=3D'-O3 -mp' FFLAGS=3D'-C90 -w90 -w95 -mp' CPICFLAGS=3D-shared > CXXPICFLAGS=3D-shared FPICFLAGS=3D-shared SHLIB_LDFLAGS=3D-shared > SHLIB_CXXLDFLAGS=3D-shared --with-blas=3D"-L/usr/lib64/GotoBLAS > -lgoto_penrynp-r1.26 -lpthread" > > I get six purported "bugs" in the config.log file (attached), but I hope > there is something I've overlooked in the past week of agony. > I have had similar log files with about 100 different combinations of > options. > I hope that you can help. > > Thank you so much. > > Tom Richards > > > ------_=_NextPart_001_01C8EAD7.27542985 > Content-Type: text/x-log; > name="config.log" > Content-Transfer-Encoding: base64 > Content-Description: config.log > Content-Disposition: attachment; > filename="config.log"[needed unpacking]