On Thursday, February 2, 2017 at 10:36:41 AM UTC, João Alberto Ferreira
wrote:
>
>
>
> On Wednesday, February 1, 2017 at 7:24:56 PM UTC+1, Dima Pasechnik wrote:
>>
>>
>>
>> On Wednesday, February 1, 2017 at 6:00:25 PM UTC, João Alberto Ferreira
>> wrote:
>>>
>>> Well, not yet.
>>>
>>> openblas has compiled successfully. The problem now is with R. The R log
>>> follows.
>>>
>>> Apparently it needs libgomp-4 and if I understood correctrly, it found
>>> an older version. But the libgomp-4 is installed
>>>
>>> [defrancaferr_joa@javel sage-7.5.1]$ rpm -q libgomp
>>> libgomp-4.4.7-17.el6.x86_64
>>>
>>
>> your log says:
>> /home/mmsim/tools/lib/64bit/libgomp.so.1 : version `GOMP_4.0' not found
>>
>> you have some rogue stuff in your PATH or something (LD_LIBRARY_PATH ?)
>>
>
> The environment variables are at the beginning of the whole log file
>
OK, I overlooked this...
>
>
> LD_LIBRARY_PATH=/opt/rh/devtoolset-3/root/usr/lib64:/opt/rh/devtoolset-3/root/usr/lib:/usr/local/lib:/home/mmsim/tools/lib/64bit
>
>
> PATH=/home/defrancaferr_joa/sage-7.5.1/build/bin:/home/defrancaferr_joa/sage-7.5.1/src/bin:/home/defrancaferr_joa/sage-7.5.1/local/bin:/opt/rh/devtoolset-3/root/usr/bin:/home/xfab/xkit/x_all/cadence/xenv:/usr/local/ADS2014_01/bin:/usr/local/texlive/2016/bin/x86_64-linux:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/defrancaferr_joa/bin:/home/eclipse:/home/matlab/bin:/home/altera/15.0/quartus/bin:/home/altera/15.0/quartus/sopc_builder/bin:/home/altera/15.0/quartus/bin:/home/ic6.1/tools/bin:/home/ic6.1/tools/dfII/bin:/home/ic6.1/tools/plot/bin:/home/ic6.1/tools/dracula/bin:/home/assura/tools/bin:/home/assura/tools/assura/bin:/home/AMS_4.10/cds/bin:/home/AMS_4.10/programs/bin:/home/mmsim/tools/bin:/home/incisiv/tools/bin:/home/incisiv/tools/dfII/bin:/home/rc/tools/bin:/home/edi/tools/bin:/home/et/tools/bin:/home/ets/tools/bin:/home/ext/tools/bin:/home/confrml/tools/bin:/home/ctos/tools/bin:/home/pve:/home/pve/tools/bin
>
>
yes, this is definitely the problem.
You can just unset these for the particular invocation of make, i.e.
export MAKE="make -j8" # or whatever numer of cores you have on the box
PATH="/bin:/usr/bin:/sbin:/usr/sbin" LD_LIBRARY_PATH="" $MAKE
Note that these wrong libraries could have been already selected by other
parts that are already built, and this may lead to hard to understand
crashes etc.
That is, I would rebuild from scratch, i.e. do first of all
make distclean
HTH
Dima
> [defrancaferr_joa@javel sage-7.5.1]$ find
> /opt/rh/devtoolset-3/root/usr/lib64/ -name "libgomp*" -exec ls -ls {} \;
> [defrancaferr_joa@javel sage-7.5.1]$ find
> /opt/rh/devtoolset-3/root/usr/lib/ -name "libgomp*" -exec ls -ls {} \;
> 4 -rw-r--r--. 1 root root 82 3 oct. 2015
> /opt/rh/devtoolset-3/root/usr/lib/gcc/x86_64-redhat-linux/4.9.2/libgomp.so
> 4 -rw-r--r--. 1 root root 169 3 oct. 2015
> /opt/rh/devtoolset-3/root/usr/lib/gcc/x86_64-redhat-linux/4.9.2/libgomp.spec
> 176 -rw-r--r--. 1 root root 178766 3 oct. 2015
> /opt/rh/devtoolset-3/root/usr/lib/gcc/x86_64-redhat-linux/4.9.2/libgomp.a
> 4 -rw-r--r--. 1 root root 78 3 oct. 2015
> /opt/rh/devtoolset-3/root/usr/lib/gcc/x86_64-redhat-linux/4.9.2/32/libgomp.so
> 140 -rw-r--r--. 1 root root 143328 3 oct. 2015
> /opt/rh/devtoolset-3/root/usr/lib/gcc/x86_64-redhat-linux/4.9.2/32/libgomp.a
> [defrancaferr_joa@javel sage-7.5.1]$ find /usr/local/lib -name "libgomp*"
> -exec ls -ls {} \;
> [defrancaferr_joa@javel sage-7.5.1]$ find /home/mmsim/tools/lib/64bit
> -name "libgomp*" -exec ls -ls {} \;
> 0 lrwxrwxrwx. 1 cadence softs 16 15 janv. 2016
> /home/mmsim/tools/lib/64bit/libgomp.so.1 -> libgomp.so.1.0.0
> 276 -rwxr-xr-x. 1 cadence softs 281302 26 sept. 2011
> /home/mmsim/tools/lib/64bit/libgomp.so.1.0.0
> 0 lrwxrwxrwx. 1 cadence softs 16 15 janv. 2016
> /home/mmsim/tools/lib/64bit/libgomp.so -> libgomp.so.1.0.0
>
>
>>
>> What is this /home/mmsim and what does it have to do with your account
>> (defrancaferr_joa, I suppose)?
>>
>
> mmsim (multi-mode simulator) is an electronic circuit simulator. I'm
> intended to use this to design an integrated circuit, but this folder
> houses an older version of the simulator (version 14). The newer version
> resides in /home/mmsim15. In fact, this machine is a new one, which the
> system administrator installed by cloning the disk of another machine. Now,
> I'm configuring it to my needs through sudo, but things seems to be
> organized in an odd manner (like this simulator in the \home directory)
>
> It seems that the configuration of the integrated circuit design tools are
> messed up and I need, at least, organize the environment variables before
> compile sage. I think I need to edit the .bash_profile (appended). What do
> you think?
>
>
>> (It finds this stuff there first, and tries to use it...)
>>
>>
>>
>>> On Wednesday, February 1, 2017 at 5:56:44 PM UTC+1, João Alberto
>>> Ferreira wrote:
>>>>
>>>> Thank you!
>>>>
>>>> I've done:
>>>>
>>>> [defrancaferr_joa@javel ~]$ sudo yum install centos-release-scl
>>>> [defrancaferr_joa@javel ~]$ sudo yum install devtoolset-3-toolchain
>>>> [defrancaferr_joa@javel ~]$ scl enable devtoolset-3 bash
>>>> [defrancaferr_joa@javel ~]$ as --version
>>>> Assembleur GNU version 2.24
>>>> Copyright 2013 Free Software Foundation, Inc.
>>>> Ce logiciel est libre; vous pouvez le redistribuer selon les termes de la
>>>> version 3 de la licence GNU General Public License ou suivante.
>>>> Ce programme n'est couvert par AUCUNE garantie.
>>>> Cet assembleur a été configuré pour la cible « x86_64-redhat-linux ».
>>>>
>>>> Let's see if it will work.
>>>>
>>>>
>>>>
>>>> On Wednesday, February 1, 2017 at 5:27:36 PM UTC+1, Dima Pasechnik
>>>> wrote:
>>>>>
>>>>>
>>>>>
>>>>> On Wednesday, February 1, 2017 at 3:52:05 PM UTC, João Alberto
>>>>> Ferreira wrote:
>>>>>>
>>>>>> Hi!
>>>>>>
>>>>>> Here it is the command output.
>>>>>>
>>>>>> [defrancaferr_joa@javel ~]$ as --version
>>>>>> GNU assembler version 2.20.51.0.2-5.44.el6 20100205
>>>>>> Copyright 2009 Free Software Foundation, Inc.
>>>>>>
>>>>>
>>>>> Thanks, this explains your problem. Your assembler is 7 years old, and
>>>>> your CPU
>>>>> is only 4 years old, if not newer. You are building with
>>>>> (sage-supplied)
>>>>> gcc 4.9, which issues correct assembler commands for your CPU.
>>>>> But your assembler does not understand some of them, as it is too old.
>>>>>
>>>>> Why Centos is so lame in this respect, we've seen many reports like
>>>>> this...
>>>>> You should upgrade your toolchain so that your assembler fully
>>>>> supports you CPU.
>>>>>
>>>>> HTH,
>>>>> Dima
>>>>>
>>>>>
>>>>>
>>>>>> This program is free software; you may redistribute it under the
>>>>>> terms of
>>>>>> the GNU General Public License version 3 or later.
>>>>>> This program has absolutely no warranty.
>>>>>> This assembler was configured for a target of `x86_64-redhat-linux'.
>>>>>>
>>>>>> On Wednesday, February 1, 2017 at 12:05:22 PM UTC+1, Dima Pasechnik
>>>>>> wrote:
>>>>>>>
>>>>>>> please post the output of
>>>>>>>
>>>>>>> as --version
>>>>>>>
>>>>>>> on the system. I guess it is too old to understand the whole range
>>>>>>> of assembler commands for your CPU.
>>>>>>>
>>>>>>>
>>>>>>> On Wednesday, February 1, 2017 at 10:09:27 AM UTC, João Alberto
>>>>>>> Ferreira wrote:
>>>>>>>>
>>>>>>>> Hi!
>>>>>>>>
>>>>>>>> I have tried to compile sagemath under a CentOS 6.8 machine, as the
>>>>>>>> binaries for Fedora do not work. The installation halted with an error
>>>>>>>> while building OpenBlas. Made the error is due to the machine CPU, as
>>>>>>>> discussed in https://github.com/JuliaLang/julia/issues/7653, but I
>>>>>>>> have little experience in this. Part of the installation log is
>>>>>>>> attached. I
>>>>>>>> updated the operating system and want to try build Sage again. Does
>>>>>>>> anyone
>>>>>>>> have any sugestion?
>>>>>>>>
>>>>>>>> It seems that all developing tools are installed, as can be seen
>>>>>>>> below
>>>>>>>>
>>>>>>>> [defrancaferr_joa@javel ~]$ rpm -q perl-ExtUtils-MakeMaker
>>>>>>>> perl-ExtUtils-MakeMaker-6.55-141.el6_7.1.x86_64
>>>>>>>> [defrancaferr_joa@javel ~]$ which perl
>>>>>>>> /usr/bin/perl
>>>>>>>> [defrancaferr_joa@javel ~]$ rpm -q binutils
>>>>>>>> binutils-2.20.51.0.2-5.44.el6.x86_64
>>>>>>>> [defrancaferr_joa@javel ~]$ rpm -q gcc
>>>>>>>> gcc-4.4.7-17.el6.x86_64
>>>>>>>> [defrancaferr_joa@javel ~]$ rpm -q make
>>>>>>>> make-3.81-23.el6.x86_64
>>>>>>>> [defrancaferr_joa@javel ~]$ rpm -q m4
>>>>>>>> m4-1.4.13-5.el6.x86_64
>>>>>>>> [defrancaferr_joa@javel ~]$ rpm -q perl
>>>>>>>> perl-5.10.1-141.el6_7.1.x86_64
>>>>>>>> [defrancaferr_joa@javel ~]$ rpm -q tar
>>>>>>>> tar-1.23-15.el6_8.x86_64
>>>>>>>> [defrancaferr_joa@javel ~]$ rpm -q git
>>>>>>>> git-1.7.1-4.el6_7.1.x86_64
>>>>>>>> [defrancaferr_joa@javel ~]$ rpm -q gcc-c++
>>>>>>>> gcc-c++-4.4.7-17.el6.x86_64
>>>>>>>> [defrancaferr_joa@javel ~]$ rpm -q gcc-gfortran
>>>>>>>> gcc-gfortran-4.4.7-17.el6.x86_64
>>>>>>>> [defrancaferr_joa@javel ~]$ rpm -q python
>>>>>>>> python-2.6.6-66.el6_8.x86_64
>>>>>>>> [defrancaferr_joa@javel ~]$ lscpu
>>>>>>>> Architecture: x86_64
>>>>>>>> CPU op-mode(s): 32-bit, 64-bit
>>>>>>>> Byte Order: Little Endian
>>>>>>>> CPU(s): 32
>>>>>>>> On-line CPU(s) list: 0-31
>>>>>>>> Thread(s) par coeur : 2
>>>>>>>> Coeur(s) par support CPU :8
>>>>>>>> Socket(s): 2
>>>>>>>> Noeud(s) NUMA : 2
>>>>>>>> ID du vendeur : GenuineIntel
>>>>>>>> Famille CPU : 6
>>>>>>>> Modèle : 79
>>>>>>>> Model name: Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz
>>>>>>>> Version : 1
>>>>>>>> CPU MHz : 1200.000
>>>>>>>> BogoMIPS: 4190.00
>>>>>>>> Virtualisation : VT-x
>>>>>>>> L1d cache : 32K
>>>>>>>> L1i cache : 32K
>>>>>>>> L2 cache : 256K
>>>>>>>> L3 cache : 20480K
>>>>>>>> NUMA node0 CPU(s): 0-7,16-23
>>>>>>>> NUMA node1 CPU(s): 8-15,24-31
>>>>>>>>
>>>>>>>
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