Problems compiling OpenMPI in SLES 11

bighoppa · 04-30-2010, 03:57 PM

Having trouble getting this app compiled and installed. It seems to be related to some kind of gcc library missing, but I went into YAST and I've installed the kernel sources, headers, devel, and a bunch of other things I found in various forums. I consistently get an error message about GLIBC_2.11 not found, even if I just do gcc -v.

Contents of config.log:

Quote:

$ ./configure --with-tm=/usr/local --prefix=/usr/local

## --------- ##
## Platform. ##
## --------- ##

hostname = cn027
uname -m = x86_64
uname -r = 2.6.27.19-5-default
uname -s = Linux
uname -v = #1 SMP 2009-02-28 04:40:21 +0100

/usr/bin/uname -p = unknown
/bin/uname -X = unknown

/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown

PATH: /sbin
PATH: /usr/sbin
PATH: /usr/local/sbin
PATH: /root/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/bin/X11
PATH: /usr/X11R6/bin
PATH: /usr/games
PATH: /usr/lib/mit/bin
PATH: /usr/lib/mit/sbin

## ----------- ##
## Core tests. ##
## ----------- ##

configure:3439: checking for a BSD-compatible install
configure:3507: result: /usr/bin/install -c
configure:3518: checking whether build environment is sane
configure:3561: result: yes
configure:3586: checking for a thread-safe mkdir -p
configure:3625: result: /bin/mkdir -p
configure:3638: checking for gawk
configure:3654: found /usr/bin/gawk
configure:3665: result: gawk
configure:3676: checking whether make sets $(MAKE)
configure:3698: result: yes
configure:3868: checking how to create a ustar tar archive
configure:3881: tar --version
tar (GNU tar) 1.20
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
configure:3884: $? = 0
configure:3924: tardir=conftest.dir && eval tar --format=ustar -chf - "$tardir"
>conftest.tar
configure:3927: $? = 0
configure:3931: tar -xf - <conftest.tar
configure:3934: $? = 0
configure:3947: result: gnutar
configure:4087: checking Open MPI version
configure:4089: result: 1.4.1
configure:4091: checking Open MPI release date
configure:4093: result: Jan 14, 2010
configure:4095: checking Open MPI Subversion repository version
configure:4097: result: r22421
configure:4199: checking Open Run-Time Environment version
configure:4201: result: 1.4.1
configure:4203: checking Open Run-Time Environment release date
configure:4205: result: Jan 14, 2010
configure:4207: checking Open Run-Time Environment Subversion repository version
configure:4209: result: r22421
configure:4311: checking Open Portable Access Layer version
configure:4313: result: 1.4.1
configure:4315: checking Open Portable Access Layer release date
configure:4317: result: Jan 14, 2010
configure:4319: checking Open Portable Access Layer Subversion repository versio
n
configure:4321: result: r22421
configure:4407: builddir: /usr/local/Downloads/openmpi-1.4.1
configure:4409: srcdir: /usr/local/Downloads/openmpi-1.4.1
configure:4431: checking build system type
configure:4449: result: x86_64-unknown-linux-gnu
configure:4491: checking host system type
configure:4506: result: x86_64-unknown-linux-gnu
configure:4706: checking whether to run code coverage
configure:4733: result: no
configure:4742: checking whether to compile with branch probabilities
configure:4754: result: no
configure:4764: checking whether to debug memory usage
configure:4776: result: no
configure:4796: checking whether to profile memory usage
configure:4808: result: no
configure:4828: checking if want developer-level compiler pickyness
configure:4840: result: no
configure:4855: checking if want developer-level debugging code
configure:4867: result: no
configure:4897: checking if want sparse process groups
configure:4909: result: no
configure:4923: checking if want Fortran 77 bindings
configure:4931: result: yes
configure:4945: checking if want Fortran 90 bindings
configure:4953: result: yes
configure:4962: checking desired Fortran 90 bindings "size"
configure:5036: result: small
configure:5043: checking whether to enable PMPI
configure:5051: result: yes
configure:5068: checking if want C++ bindings
configure:5076: result: yes
configure:5085: checking if want MPI::SEEK_SET support
configure:5093: result: yes
configure:5111: checking if want to enable weak symbol support
configure:5119: result: yes
configure:5132: checking if want run-time MPI parameter checking
configure:5153: result: runtime
configure:5176: checking if want to install OMPI header files
configure:5189: result: no
configure:5205: checking if want pretty-print stacktrace
configure:5217: result: yes
configure:5231: checking if peruse support is required
configure:5243: result: no
configure:5266: checking max supported array dimension in F90 MPI bindings
configure:5302: result: 4
configure:5307: checking if pty support should be enabled
configure:5319: result: yes
configure:5332: checking if user wants dlopen support
configure:5347: result: yes
configure:5355: checking if heterogeneous support should be enabled
configure:5367: result: no
configure:5381: checking if want trace file debugging
configure:5393: result: no
configure:5407: checking if want full RTE support
configure:5426: result: yes
configure:5497: checking if want fault tolerance
configure:5510: result: Disabled fault tolerance
configure:5627: checking if want IPv6 support
configure:5639: result: yes (if underlying system supports it)
configure:5652: checking if want orterun "--prefix" behavior to be enabled by de
fault
configure:5672: result: no
configure:5685: checking for package/brand string
configure:5701: result: Open MPI root@cn027 Distribution
configure:5707: checking for ident string
configure:5724: result: 1.4.1
configure:5731: checking whether to add padding to the openib control header
configure:5744: result: no
configure:5758: checking whether to use an alternative checksum algo for message
s
configure:5771: result: no
configure:5993: checking for style of include used by make
configure:6021: result: GNU
configure:6096: checking for gcc
configure:6112: found /usr/local/bin/gcc
configure:6123: result: gcc
configure:6355: checking for C compiler version
configure:6363: gcc --version >&5
gcc: /lib64/libc.so.6: version `GLIBC_2.11' not found (required by gcc)
configure:6367: $? = 1
configure:6374: gcc -v >&5
gcc: /lib64/libc.so.6: version `GLIBC_2.11' not found (required by gcc)
configure:6378: $? = 1
configure:6385: gcc -V >&5
gcc: /lib64/libc.so.6: version `GLIBC_2.11' not found (required by gcc)
configure:6389: $? = 1
configure:6412: checking for C compiler default output file name
configure:6434: gcc -DNDEBUG conftest.c >&5
gcc: /lib64/libc.so.6: version `GLIBC_2.11' not found (required by gcc)
configure:6438: $? = 1
configure:6476: result:
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "Open MPI"
| #define PACKAGE_TARNAME "openmpi"
| #define PACKAGE_VERSION "1.4.1"
| #define PACKAGE_STRING "Open MPI 1.4.1"
| #define PACKAGE_BUGREPORT "http://www.open-mpi.org/community/help/"
| #define OMPI_MAJOR_VERSION 1
| #define OMPI_MINOR_VERSION 4
| #define OMPI_RELEASE_VERSION 1
| #define OMPI_GREEK_VERSION ""
| #define OMPI_VERSION "1"
| #define OMPI_RELEASE_DATE "Jan 14, 2010"
| #define ORTE_MAJOR_VERSION 1
| #define ORTE_MINOR_VERSION 4
| #define ORTE_RELEASE_VERSION 1
| #define ORTE_GREEK_VERSION ""
| #define ORTE_VERSION "1"
| #define ORTE_RELEASE_DATE "Jan 14, 2010"
| #define OPAL_MAJOR_VERSION 1
| #define OPAL_MINOR_VERSION 4
| #define OPAL_RELEASE_VERSION 1
| #define OPAL_GREEK_VERSION ""
| #define OPAL_VERSION "1"
| #define OPAL_RELEASE_DATE "Jan 14, 2010"
| #define OMPI_ARCH "x86_64-unknown-linux-gnu"
| #define OMPI_ENABLE_MEM_DEBUG 0
| #define OMPI_ENABLE_MEM_PROFILE 0
| #define OMPI_ENABLE_DEBUG 0
| #define OMPI_GROUP_SPARSE 0
| #define OMPI_WANT_MPI_CXX_SEEK 1
| #define MPI_PARAM_CHECK ompi_mpi_param_check
| #define OMPI_WANT_PRETTY_PRINT_STACKTRACE 1
| #define OMPI_WANT_PERUSE 0
| #define OMPI_ENABLE_PTY_SUPPORT 1
| #define OMPI_ENABLE_HETEROGENEOUS_SUPPORT 0
| #define OPAL_ENABLE_TRACE 0
| #define ORTE_DISABLE_FULL_SUPPORT 0
| #define OPAL_ENABLE_FT 0
| #define OPAL_ENABLE_FT_CR 0
| #define OMPI_WANT_HOME_CONFIG_FILES 1
| #define OPAL_ENABLE_IPV6 1
| #define ORTE_WANT_ORTERUN_PREFIX_BY_DEFAULT 0
| #define OPAL_PACKAGE_STRING "Open MPI root@cn027 Distribution"
| #define OPAL_IDENT_STRING "1.4.1"
| #define OMPI_OPENIB_PAD_HDR 0
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:6482: error: in `/usr/local/Downloads/openmpi-1.4.1':
configure:6485: error: C compiler cannot create executables
See `config.log' for more details.

Etc.

Any ideas on what I'm missing to get stuff to compile?

knudfl · 04-30-2010, 06:15 PM

Welcome to LQ.

A missing glibc-devel ?? .... # zypper in glibc-devel

You may also need the gcc33-fortran-3.3.3-15.3.x86_64.rpm
( from suse 11.2 )
.. providing /usr/bin/g77-33 , for the fortran 77 files.
http://download.opensuse.org/distrib...s/suse/x86_64/

Also required, for dependency :
cpp33-3.3.3-15.3.x86_64.rpm , gcc33-3.3.3-15.3.x86_64.rpm
..

bighoppa · 05-03-2010, 08:20 AM

glibc-devel is already installed. I doubled checked and ran zypper anyway, but that just confirmed it. I added in the other packages above and it still won't compile.

knudfl · 05-04-2010, 03:21 AM

" Suse SLED 11 " has 'glibc-2.9'.

Something funny is going on, when 'gcc -v' asks for GLIBC_2.11.

Where did you get that gcc ? ?

Please post the output of : rpm -qa | grep gcc
.. And : rpm -qa | grep glibc
..

bighoppa · 05-04-2010, 09:12 AM

I think i dl'ed an update package for gcc at some point. Can't remember where I got it from, but I think maybe it was this package:'gcc-4.5-x86_64.tar.gz'. I've put in several different packages trying to get this sorted out, so I may just have a mess on my hands that I'll need to reimage the node.

Output of rpm -qa | grep gcc:

Quote:

gcc-32bit-4.3-62.198
gcc43-info-4.3.3_20081022-11.18
gcc43-32bit-4.3.3_20081022-11.18
gcc43-locale-4.3.3_20081022-11.18
gcc-info-4.3-62.198
gcc33-3.3.3-15.3
libgcc44-4.4.1_20090817-2.3.4
libgcc43-32bit-4.3.3_20081022-11.18
gcc43-4.3.3_20081022-11.18
gcc-locale-4.3-62.198
libgcc43-4.3.3_20081022-11.18
gcc43-c++-4.3.3_20081022-11.18
gcc33-fortran-3.3.3-15.3
gcc44-4.4.1_20090817-2.3.4
gcc-4.3-62.198
gcc-c++-4.3-62.198

Output of rpm -qa | grep glibc:

Quote:

glibc-locale-32bit-2.9-13.2
glibc-i18ndata-2.9-13.2
glibc-devel-2.9-13.2
glibc-locale-2.9-13.2
glibc-2.9-13.2
glibc-devel-32bit-2.9-13.2
glibc-32bit-2.9-13.2

Thanks for the help.

knudfl · 05-04-2010, 01:02 PM

"gcc44-4.4.1_20090817-2.3.4" looks like a Suse 11.2 OSS package.
... Created with glibc-2.11 it may be a Suse 11.3 package ?

Not usable ! Must be removed.
# zypper rm gcc44

And the gcc43-4.3.3_20081022-11.18 must be reinstalled.
1) # rpm -e --nodeps gcc43
2) # zypper in gcc43
..

bighoppa · 05-04-2010, 02:46 PM

Removing gcc44 and reinstalling gcc43 didn't work, but I think you were on the right track. One of the packages hosed up glibc.

I started over with a fresh install from disk and installed gcc, gcc43, gcc++, gcc43-c++, and associated dependencies from YAST. I also installed libgfortran44 and libreadline6. the .configure ran perfectly and the make just completed as well.

Thanks a ton for all the help, knudfl! I owe you a beer!