[mvapich-discuss] Mvapich building errors

Subramoni, Hari subramoni.1 at osu.edu
Wed Oct 17 09:47:22 EDT 2018 

Dear, Lorenzo.


You can use the script below to build and install the necessary version of autotools. After installing these, please try the configure step with the latest MVAPICH2 2.3GA tarball.



If you invoke it as <script_file_name.sh> $PWD, it will install everything under $PWD/Tools/install-dir. You can then add $PWD/Tools/install-dir/bin to $PATH and $PWD/Tools/install-dir/lib to LD_LIBRARY_PATH and run autogen.sh



#!/bin/bash



#set -x



#Error checking

if [ ! -n "$1" ]

then

    echo "Please pass the base dir and re-run script"

    exit 1

fi



base_dir="$1/Tools"



gnum4_path="$base_dir/GNUM4"

autoconf_path="$base_dir/Autoconf"

automake_path="$base_dir/Automake"

libtool_path="$base_dir/Libtool"



install_dir="$base_dir/install-dir"



gnum4_version="m4-1.4.17"

autoconf_version="autoconf-2.69"

automake_version="automake-1.15"

libtool_version="libtool-2.4.6"



gnum4_repo="http://ftp.gnu.org/gnu/m4/$gnum4_version.tar.gz"

autoconf_repo="http://ftp.gnu.org/gnu/autoconf/$autoconf_version.tar.gz"

automake_repo="http://ftp.gnu.org/gnu/automake/$automake_version.tar.gz"

libtool_repo="https://ftp.gnu.org/gnu/libtool/$libtool_version.tar.gz"



error_print()

{

    step=$1

    repo_name=$2

    err_code=$3

    if [ "$err_code" -ne "0" ]

    then

            echo "$step for $repo_name failed"

            cd -

            exit 1

    else

        if [ "$VERBOSE" == "1" ]

        then

                echo "$step for $repo_name succeeded"

       fi

    fi

}



install_library()

{

    repo=$1

    repo_name=$2

    local_path=$3



    cd $local_path

    wget $repo >& /dev/null

    error_print "wget" $repo_name $?



    tar -zxvf "$repo_name.tar.gz"  >& /dev/null

    error_print "un-tar" $repo_name $?



    cd $repo_name



    ./configure --prefix=$install_dir >& /dev/null

    error_print "configure" $repo_name $?



    make clean &> /dev/null

    error_print "make clean" $repo_name $?



    make &> /dev/null

    error_print "make" $repo_name $?



    make install &> /dev/null

    error_print "make install" $repo_name $?



    cd - >& /dev/null

}



mkdir -p $gnum4_path $autoconf_path $automake_path $libtool_path $install_dir



#Install GNU M4

install_library $gnum4_repo $gnum4_version $gnum4_path echo "$gnum4_version installed successfully"



#Install Autoconf

install_library $autoconf_repo $autoconf_version $autoconf_path echo "$autoconf_version installed successfully"



#Install Libtool

install_library $libtool_repo $libtool_version $libtool_path echo "$libtool_version installed successfully"



#Install Automake

install_library $automake_repo $automake_version $automake_path echo "$automake_version installed successfully"


Thx,
Hari.

From: Lorenzo Varriale <lorenzo.varriale at prismaspa.it>
Sent: Wednesday, October 17, 2018 9:05 AM
To: Subramoni, Hari <subramoni.1 at osu.edu>
Cc: mvapich-discuss at cse.ohio-state.edu <mvapich-discuss at mailman.cse.ohio-state.edu>
Subject: Re: [mvapich-discuss] Mvapich building errors

Hari,

Here’s the output from autopen.sh ;


[root at cn01 mvapich2-2.2rc1-gcc-485-cuda8]# ./autogen.sh

####################################
## Replicating confdb (and similar)
####################################

syncing 'src/mpl' --> 'src/pm/hydra/mpl'
syncing 'confdb' --> 'src/mpi/romio/confdb'
syncing 'confdb' --> 'src/mpl/confdb'
syncing 'confdb' --> 'src/pm/hydra/confdb'
syncing 'confdb' --> 'src/pm/hydra/mpl/confdb'
syncing 'confdb' --> 'test/mpi/confdb'

####################################
## Checking user environment
####################################

Verifying the location of autogen.sh... done
Checking if autotools are in the same location... yes, all in /usr
Checking for autoconf version... >= 2.67
Checking for automake version... bad automake installation
You either do not have automake in your path or it is too old (version
1.15 or higher required). You may be able to use

     automake --version

Unfortunately, there is no standard format for the version output and
it changes between autotools versions.  In addition, some versions of
autoconf choose among many versions and provide incorrect output).
[root at cn01 mvapich2-2.2rc1-gcc-485-cuda8]#

Yesterday we already stumbled in automake issues, hence we started some researches as per the yum available packages but, sadly, we still aren’t able to find a suitable version like the one suggested by autopen.

[root at cn01 mvapich2-2.2rc1-gcc-485-cuda8]# yum provides */automake
Plugin abilitati:fastestmirror, langpacks
Loading mirror speeds from cached hostfile
 * base: ba.mirror.garr.it<http://ba.mirror.garr.it>
 * epel: epel.besthosting.ua<http://epel.besthosting.ua>
 * extras: ba.mirror.garr.it<http://ba.mirror.garr.it>
 * updates: centos.mirror.ptisp.pt<http://centos.mirror.ptisp.pt>
automake-1.13.4-3.el7.noarch : A GNU tool for automatically creating Makefiles
Repo         : base
Corrispondenza trovata in:
Nome file   : /usr/bin/automake



1:bash-completion-extras-2.1-11.el7.noarch : Additional programmable completions for Bash
Repo         : epel
Corrispondenza trovata in:
Nome file   : /usr/share/bash-completion/completions/automake



automake-1.13.4-3.el7.noarch : A GNU tool for automatically creating Makefiles
Repo         : @anaconda
Corrispondenza trovata in:
Nome file   : /usr/bin/automake



[root at cn01 mvapich2-2.2rc1-gcc-485-cuda8]# yum search automake
Plugin abilitati:fastestmirror, langpacks
Loading mirror speeds from cached hostfile
 * base: ba.mirror.garr.it<http://ba.mirror.garr.it>
 * epel: epel.besthosting.ua<http://epel.besthosting.ua>
 * extras: ba.mirror.garr.it<http://ba.mirror.garr.it>
 * updates: centos.mirror.ptisp.pt<http://centos.mirror.ptisp.pt>
=================================================================== N/S matched: automake ====================================================================
automake.noarch : A GNU tool for automatically creating Makefiles

  Ricerca effettuata solamente in nome e descrizione breve, usare "search all" per cercare in tutti i campi.
[root at cn01 mvapich2-2.2rc1-gcc-485-cuda8]# yum info automake
Plugin abilitati:fastestmirror, langpacks
Loading mirror speeds from cached hostfile
 * base: ba.mirror.garr.it<http://ba.mirror.garr.it>
 * epel: epel.besthosting.ua<http://epel.besthosting.ua>
 * extras: ba.mirror.garr.it<http://ba.mirror.garr.it>
 * updates: centos.mirror.ptisp.pt<http://centos.mirror.ptisp.pt>
Pacchetti installati
Nome         : automake
Arch         : noarch
Versione     : 1.13.4
Rilascio     : 3.el7
Dimensione   : 1.7 M
Repo         : installed
Dal repo     : anaconda
Sommario     : A GNU tool for automatically creating Makefiles
URL          : http://www.gnu.org/software/automake/
Licenza      : GPLv2+ and GFDL and Public Domain and MIT
Descrizione  : Automake is a tool for automatically generating `Makefile.in<http://Makefile.in>'
             : files compliant with the GNU Coding Standards.
             :
             : You should install Automake if you are developing software and would
             : like to use its ability to automatically generate GNU standard
             : Makefiles.

[root at cn01 mvapich2-2.2rc1-gcc-485-cuda8]#

How can we go further in investigation? Shall we download a newer version of automake from a different repo?

Best,

Lorenzo.




Il giorno 17 ott 2018, alle ore 13:23, Subramoni, Hari <subramoni.1 at osu.edu<mailto:subramoni.1 at osu.edu>> ha scritto:

Hi, Lorenzo.

Can you please try the following series of commands?

./autogen.sh
./configure …
make
make install

These are warnings seen during the autogen step. We had fixed this with the 2.3GA release. Can you please let us know if you still see the errors after you do these steps?

On a different note, if you are using the release tarball from our website, you need not do the autogen.sh (or the autoreconf -if) step. You can directly start from configure.

Best Regards,
Hari.

From: mvapich-discuss-bounces at cse.ohio-state.edu<mailto:mvapich-discuss-bounces at cse.ohio-state.edu> On Behalf Of Lorenzo Varriale
Sent: Wednesday, October 17, 2018 3:54 AM
To: mvapich-discuss at cse.ohio-state.edu<mailto:mvapich-discuss at cse.ohio-state.edu> <mvapich-discuss at mailman.cse.ohio-state.edu<mailto:mvapich-discuss at mailman.cse.ohio-state.edu>>
Subject: [mvapich-discuss] Mvapich building errors

Greetings Team,

We’re currently having issues in building several versions of mvapich on our cluster, the more we try, the less we achieve. Actually, we are at a loss, any suggestion is very appreciated.

Following, some details about errors and environment we have on our cluster:

MVAPICH2 V2.2rc1, 2.2, 2.3

##modules loaded

gcc 4.8.5
cuda 8.0

###command issues

autoreconf -f -i

./configure --prefix=/home/share/opt/mvapich2-2.2-gcc-485-cuda8 F77=gfortran FC=gfortran CPP=cpp CC=gcc CXX=c++ LDFLAGS="-L/lib -L/home/share/nvidia/cuda-8.0/lib64" --enable-cuda=basic --with-cuda=/home/share/nvidia/cuda-8.0

Make output error:

[root at cn01 mvapich2-2.2rc1-gcc-485-cuda8]# make
( cd . && rm -f .err unusederr.txt ; rm -rf .tmp )
( cd . && \
  ./maint/extracterrmsgs -careful=unusederr.txt \
                         -skip=src/util/multichannel/mpi.c \
                         `cat maint/errmsgdirs` > .tmp 2>.err )
( cd . && if test -s .err ; then rm -f .tmp ; cat .err ; exit 1 ; fi )
Warning: attempt to redefine **rdmacmmaxport.  Duplicate ignored.
Warning: attempt to redefine **rdmacmmaxport %d %d %d.  Duplicate ignored.
Warning: attempt to redefine **rdmacmminport.  Duplicate ignored.
Warning: attempt to redefine **rdmacmminport %d %d %d.  Duplicate ignored.
Warning: attempt to redefine **rdmacminvalidport.  Duplicate ignored.
Warning: attempt to redefine **rdmacminvalidport %d.  Duplicate ignored.
Warning: attempt to redefine **rdmacmportrange.  Duplicate ignored.
Warning: attempt to redefine **rdmacmportrange %d %d.  Duplicate ignored.
Warning: attempt to redefine **activeports.  Duplicate ignored.
Warning: attempt to redefine **activeports %d.  Duplicate ignored.
Warning: attempt to redefine **ibv_get_device_name.  Duplicate ignored.
Warning: attempt to redefine **onesidedcomps.  Duplicate ignored.
Warning: attempt to redefine **portquery.  Duplicate ignored.
Warning: attempt to redefine **portquery %d.  Duplicate ignored.
Warning: attempt to redefine **rdmacmmaxport.  Duplicate ignored.
Warning: attempt to redefine **rdmacmmaxport %d %d %d.  Duplicate ignored.
Warning: attempt to redefine **rdmacmminport.  Duplicate ignored.
Warning: attempt to redefine **rdmacmminport %d %d %d.  Duplicate ignored.
Warning: attempt to redefine **rdmacminvalidport.  Duplicate ignored.
Warning: attempt to redefine **rdmacminvalidport %d.  Duplicate ignored.
Warning: attempt to redefine **rdmacmportrange.  Duplicate ignored.
Warning: attempt to redefine **rdmacmportrange %d %d.  Duplicate ignored.
Warning: attempt to redefine **umadgetca.  Duplicate ignored.
Warning: attempt to redefine **umadgetrate.  Duplicate ignored.
Warning: attempt to redefine **umadinit.  Duplicate ignored.
make: *** [src/mpi/errhan/defmsg.h] Error 1

Other system infos:

[root at cn01 mvapich2-2.2rc1-gcc-485-cuda8]# uname -a
Linux cn01 3.10.0-514.el7.x86_64 #1 SMP Tue Nov 22 16:42:41 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

[root at cn01 mvapich2-2.2rc1-gcc-485-cuda8]# automake --version
automake (GNU automake) 1.13.4

[root at cn01 mvapich2-2.2rc1-gcc-485-cuda8]# rpm -qa | grep -i ofed
mlnx-ofa_kernel-3.4-OFED.3.4.2.0.0.1.g30039f7.rhel7u3.x86_64
knem-mlnx-1.1.2.90mlnx1-OFED.3.3.1.5.5.1.ga659703.rhel7u3.x86_64
kmod-isert-1.7-OFED.3.4.1.0.6.1.g30039f7.rhel7u3.x86_64
ofed-scripts-3.4-OFED.3.4.2.0.0.x86_64
libibverbs-utils-1.2.1mlnx1-OFED.3.4.0.1.4.34200.x86_64
libmlx5-devel-1.2.1mlnx1-OFED.3.4.1.0.0.34200.x86_64
librdmacm-utils-1.1.0mlnx-OFED.3.4.0.0.4.34200.x86_64
dapl-2.1.9mlnx-OFED.3.3.0.0.6.34100.x86_64
kmod-mlnx-ofa_kernel-3.4-OFED.3.4.2.0.0.1.g30039f7.rhel7u3.x86_64
kmod-knem-mlnx-1.1.2.90mlnx1-OFED.3.3.1.5.5.1.ga659703.rhel7u3.x86_64
kmod-srp-1.6.1-OFED.3.4.1.0.6.1.g30039f7.rhel7u3.x86_64
kmod-mlnx-sdp-3.4-OFED.3.4.1.0.6.1.g30039f7.rhel7u3.x86_64
libibverbs-1.2.1mlnx1-OFED.3.4.0.1.4.34200.x86_64
libibverbs-devel-static-1.2.1mlnx1-OFED.3.4.0.1.4.34200.x86_64
libmlx4-1.2.1mlnx1-OFED.3.4.0.0.4.34200.x86_64
libmlx5-1.2.1mlnx1-OFED.3.4.1.0.0.34200.x86_64
libibcm-1.0.5mlnx2-OFED.3.4.0.0.4.34100.x86_64
librdmacm-1.1.0mlnx-OFED.3.4.0.0.4.34200.x86_64
librdmacm-devel-1.1.0mlnx-OFED.3.4.0.0.4.34200.x86_64
libsdp-devel-1.1.108-OFED.3.0.8.gfbd01df.34100.x86_64
dapl-devel-2.1.9mlnx-OFED.3.3.0.0.6.34100.x86_64
dapl-utils-2.1.9mlnx-OFED.3.3.0.0.6.34100.x86_64
mlnxofed-docs-3.4-2.0.0.0.noarch
mlnx-ofa_kernel-devel-3.4-OFED.3.4.2.0.0.1.g30039f7.rhel7u3.x86_64
kmod-iser-1.8.1-OFED.3.4.1.0.6.1.g30039f7.rhel7u3.x86_64
kmod-mlnx-rds-3.4-OFED.3.4.1.0.6.1.g30039f7.rhel7u3.x86_64
libibverbs-devel-1.2.1mlnx1-OFED.3.4.0.1.4.34200.x86_64
libmlx4-devel-1.2.1mlnx1-OFED.3.4.0.0.4.34200.x86_64
libibcm-devel-1.0.5mlnx2-OFED.3.4.0.0.4.34100.x86_64
ibacm-1.2.1mlnx1-OFED.3.4.0.1.5.34100.x86_64
libsdp-1.1.108-OFED.3.0.8.gfbd01df.34100.x86_64
dapl-devel-static-2.1.9mlnx-OFED.3.3.0.0.6.34100.x86_64


Thanks in advance,

Lorenzo Varriale.

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