topic Re: Installation and runtime issues in openSUSE 11.1 in Intel® Fortran Compiler

Installation and runtime issues in openSUSE 11.1

rkanna2 — Wed, 18 Mar 2009 15:06:59 GMT

I tried to install Fortran compiler version 11.081 (intel64) in Linux OS, openSUSE 11.1 (64-Bit) version. My machine is intel Core 2 Duo. I have provided below a transcript of online chat.

When I tried to install the Fortran Compiler, I had three warnings.

1. OS is NOT recognized by installer.
2. glibc version (2.9) installed in PC is NOT recognized by the installer
3. Binutils and binutils-delevel version (2.19) are NOT recognized by the installer.

I already installed libstdc++33 and libstdc++33-32bit through Yast. These contain the library libstdc++.so.5

I ignored the three warnings and installed the compiler. Then I compiled a scientific application in fortran which contains only OPENMP directives and NO MPI. I had no error messages during compiling. However during run time I get the following error when I set 'setenv OMP_NUM_THREADS 2'.

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libpthread.so.0 00007FD5C759892B Unknown Unknown Unknown
libguide.so 00007FD5C789C3FE Unknown Unknown Unknown

I have the following flags in my makefile.

LDFLAGS = -Wl,-Bstatic -Wl,--start-group -L ${MKL_HOME}/lib/em64t -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic -lguide -lpthread

Can you let me know if there is any workaround for this problem, since glibc is NOT recognized by installer. Is libpthread.so.0 part of glibc or Binutils?

Any help in this regard will be appreciated.

Re: Installation and runtime issues in openSUSE 11.1

TimP — Wed, 18 Mar 2009 16:48:26 GMT

1. OpenSuSE (all versions) is flagged as not recognized, to alert you that this OS has not been tested.
2. the glibc is too new to have been tested. That doesn't mean it may not work. libpthread is part of glibc.
3. binutils recognition is a persistent Intel installer bug, which shows up in all unsupported OS. I use binutils 2.19.50 successfully, on OpenSuSE 10.3 and RHEL5.2, and before that 2.19 was OK as far as I know.

I don't think you should install a libstdc++ which doesn't match your g++ installation. It shouldn't matter unless you have linked C++ objects in your project. I assumed the libstdc++ in the ifort installer were meant for one specific brand of g++ build, and the installer would take care of that special situation; I've never seen it used.

For additional hints on MKL link setup, you should read the notes in mkl docs directory, and consult MKL forum. You might check your ability to get it working with the most basic (default) dynamic link setup, using ifort -openmp option in place of -lguide -lpthread. libguide is for backward compatibility with ifort 10.0. Don't try to combine features of the static and dynamic MKL link procedures, at least not until you have tried the standard ways. Your problem could be due to your link command.

Re: Installation and runtime issues in openSUSE 11.1

rkanna2 — Wed, 18 Mar 2009 20:52:59 GMT

Hi Tim,

I am a bit new to Linux system. The makefile I use is as follows.

--------------------------------------------------------------
FINCLUDE = $(wildcard $(SIHOME)opemp/*.f)
FMODULE = $(wildcard $(SIHOME)opemp/mod/*.f)
SOURCES = $(wildcard *.f)
HEADER_FILES = $(wildcard *.h)
OBJS = $(FINCLUDE:.f=.o)
OBJSMOD = $(FMODULE:.f=.o)
FL = built_objs

OBJS_PROD = $(SOURCES:.f=.o)

EXEC_NAME = Silicon

F = ifort -openmp -ipo -traceback

OPTI = -O0 -ftz -C # try -O2 , with/without -ftz, adding -mp

LDFLAGS = -L ${MKL_HOME}/lib/em64t -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core

prod : $(EXEC_NAME)

all : prod

clean :
rm -f *.o *.mod $(EXEC_NAME)

$(EXEC_NAME) : $(OBJSMOD) $(OBJS_PROD) $(OBJS)
$(F) $(OPTI) -o $(EXEC_NAME) $(wildcard *.o) $(LDFLAGS)

%.o : %.f
$(F) $(OPTI) -c -g $?
-----------------------------------------------------------------------------

I still get the same error. I have used dynamic linking as given in the mkl documentation.

-----------------------------------------
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libpthread.so.0 00007F6E6C83292B Unknown Unknown Unknown
libiomp5.so 00007F6E6CAAA89E Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
------------------------------------------------

Re: Installation and runtime issues in openSUSE 11.1

rkanna2 — Wed, 18 Mar 2009 21:31:43 GMT

I have installed 64-bit version of openSUSE.

uname -a
Linux comp.name 2.6.27.19-3.2-default #1 SMP 2009-02-25 15:40:44 +0100 x86_64 x86_64 x86_64 GNU/Linux

Re: Installation and runtime issues in openSUSE 11.1

TimP — Thu, 19 Mar 2009 04:21:57 GMT

Don't see anything obviously wrong, other than it being too complicated even for experienced Makefile users, with options apparently combined in random ways. What does the build log look like? Do you get any clues by running under debugger?