Problems Compiling Milonga

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Hector Lestani

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Feb 14, 2019, 1:37:00 PM2/14/19
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Dear all,
I am having problems to compile milonga.

First, an error message in the Makefile was appearing. Two tabs have
been added to the file "milonga/src/Makefile"  lines 2318 and 2319 (one
tab each), to avoid error and abort messages.

Then, some headers (*.h) were not found due to missing paths. To solve
this, I added the directories "petsc-3.10.3/include" and
"petsc-3.10.3/arch-linux2-c-debug/include" to the variable
"$PETSC_CC_INCLUDES" in file "~/.bashrc". And also added the directories
"slepc-3.10.2/include" and "slepc-3.10.2/arch-linux2-c-debug/include" to
the variable "$SLEPC_CC_INCLUDES" in file "~/.bashrc".

But now, some linking problems arose. It says that
./milonga-version.o: In function 'plugin_longversion':
version.c:(.text+0x56): undefined reference to 'PetscGetVersion'

I think that a "-L" argument might be missing in the Makefile, but I'm
not sure where to point that.

Any comments are welcome, any.

Thanks in advance,
Regards.

Hector Lestani

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Feb 14, 2019, 1:44:59 PM2/14/19
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Sorry,
I'm talking about the last commit available:
fr@fr-VirtualBox ~/milonga $ git log
commit 04b0ee5facef0e1cd7fee139927c4d9899d15872
Author: gtheler <jer...@seamplex.com>
Date:   Mon Feb 4 08:23:57 2019 -0300

Jeremy Theler

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Feb 14, 2019, 1:57:21 PM2/14/19
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On Thu, 2019-02-14 at 15:33 -0300, Hector Lestani wrote:
Dear all,
I am having problems to compile milonga.

what operating system?

First, an error message in the Makefile was appearing. Two tabs have 
been added to the file "milonga/src/Makefile"  lines 2318 and 2319 (one 
tab each), to avoid error and abort messages.

hint: if you need to tweak a Makefile then do expect further errors.

Then, some headers (*.h) were not found due to missing paths. To solve 
this, I added the directories "petsc-3.10.3/include" and 
"petsc-3.10.3/arch-linux2-c-debug/include" to the variable 
"$PETSC_CC_INCLUDES" in file "~/.bashrc". And also added the directories 
"slepc-3.10.2/include" and "slepc-3.10.2/arch-linux2-c-debug/include" to 
the variable "$SLEPC_CC_INCLUDES" in file "~/.bashrc".

I am assuming you want to link against PETSc 3.10.3 and SLEPc 3.10.2 which have been configured and compiled by you, i.e. they are not provided by the package manager in a global location like /usr or so.

Set PETSC_DIR and SLEPC_DIR to their directories. Mine are:

gtheler@tom:~/codigos/wasora-suite/milonga$ export PETSC_DIR=/home/gtheler/libs/petsc-3.10.3
gtheler@tom:~/codigos/wasora-suite/milonga$ export SLEPC_DIR=/home/gtheler/libs/slepc-3.10.2

The default PETSC_ARCH is

gtheler@tom:~/codigos/wasora-suite/milonga$ export PETSC_ARCH=arch-linux2-c-debug

Now autogen, configure and make:

gtheler@tom:~/codigos/wasora-suite/milonga$ ./autogen.sh
gtheler@tom:~/codigos/wasora-suite/milonga$ ./configure
gtheler@tom:~/codigos/wasora-suite/milonga$ make    

No error whatsoever, and it is indeed linked against the given versions:
gtheler@tom:~/codigos/wasora-suite/milonga$ ./milonga -i
milonga v0.5.58-g04b0ee5  
free nuclear reactor core analysis code


last commit on Mon Feb 4 08:23:57 2019 -0300
compiled on 2019-02-14 15:56:30 by gtheler@tom ( )
with gcc (Debian 6.3.0-18+deb9u1) 6.3.0 20170516 using -O2 linked against
 SLEPc Release Version 3.10.2, feb 11, 2019
 Petsc Release Version 3.10.3, Dec, 18, 2018  arch-linux2-c-debug
running on Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.130-2 (2018-10-27) x86_64
8  Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz


---------         --------        --------      ---   ---    
wasora v0.5.291-gffe3d44  
wasora’s an advanced suite for optimization & reactor analysis

Last commit date   : Wed Feb 13 08:51:54 2019 -0300
Build date         : 2019-02-14 15:54:23
Build architecture :   
Builder            : gtheler@tom
GSL version        : 2.3
SUNDIALs version   : 2.5.0
Readline version   : 7.0
gtheler@tom:~/codigos/wasora-suite/milonga$ 




But now, some linking problems arose. It says that
./milonga-version.o: In function 'plugin_longversion':
version.c:(.text+0x56): undefined reference to 'PetscGetVersion'

I think that a "-L" argument might be missing in the Makefile, but I'm 
not sure where to point that.

Any comments are welcome, any.

What is wrong with using PETSc and SLEPc as provided by your OS's package manager as suggesed in the webpage?
Make sure both PETSC_DIR and SLEPC_DIR are empty and follow the instructions from the webpage.

sudo apt-get install m4 make autoconf automake gcc g++ git findutils
sudo apt-get install libgsl-dev libsundials-serial-dev libreadline-dev petsc-dev slepc-dev
git clone https://bitbucket.org/seamplex/milonga/
cd milonga
./autogen.sh
./configure
make
make check



Thanks in advance,
Regards.


Hector Lestani
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Feb 14, 2019, 2:19:14 PM2/14/19
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    Thanks for the prompt answer Germán.

    

    I am doing all this in Linux Mint Rosa.

    

    I had no option but to touch the makefile, it was complaining.

    Yes, I want to link against PETSc 3.10.3 and SLEPc 3.10.2, which I
    downloaded and compiled, because the package manager suggests me to
    install version 3.4.2, which is too old, I think. Do you think I
    could use that version for the current commit of milonga?

    

    I didn't empty the PETSC_DIR and SLEPC_DIR variables before
    compiling those libraries, could it be the problem? I'll try that
    and report.

    

    Thanks.

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jeremy theler
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Feb 14, 2019, 2:25:22 PM2/14/19
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3.4 is too old, can't you switch to a newer distro?

if not, you are right, you need to download and compile petsc and slepc yourself
just set tland export the three variables and it should work as I showed

if it does not please provide all the commands you issue and the errors you get but do not modify the makefiles


-- 
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jeremy theler
www.seamplex.com


jeremy theler
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Feb 14, 2019, 2:45:33 PM2/14/19
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btw make was complaining because of some other error, not because there is something wrong in the milonga repository

the actual makefile is generated by automake from makefile.in

On Thu, Feb 14, 2019, 16:19 Hector Lestani <lest...@cab.cnea.gov.ar> wrote:
César Pablo Camusso
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Feb 15, 2019, 6:40:39 AM2/15/19
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Hello.
I updated it with:
git pull
./autogen
./configure
make
make check

============================================================================
Testsuite summary for milonga v0.5.58-g04b0ee5
============================================================================
# TOTAL: 3
# PASS:  3
# SKIP:  0
# XFAIL: 0
# FAIL:  0
# XPASS: 0
# ERROR: 0
============================================================================


pablo@debian:~/petsc/wasora-suite/milonga$ ./milonga -v
milonga v0.5.58-g04b0ee5+Δ 
free nuclear reactor core analysis code

 last commit on Mon Feb 4 08:23:57 2019 -0300
 compiled on 2019-02-15 08:44:38 by pablo@debian ( )
 with gcc (Debian 4.9.2-10+deb8u1) 4.9.2 using -O2 linked against
  SLEPc Release Version 3.7.3, Sep 29, 2016
  Petsc Release Version 3.7.4, Oct, 02, 2016  arch-linux2-c-opt
 running on Linux 3.16.0-7-amd64 #1 SMP Debian 3.16.59-1 (2018-10-03) x86_64
 4  Intel(R) Core(TM) i3-4130 CPU @ 3.40GHz


 milonga is copyright (c) 2010-2018 jeremy theler
 licensed under GNU GPL version 3 or later.
 milonga is free software: you are free to change and redistribute it.
 There is NO WARRANTY, to the extent permitted by law.


-----------------           -----------          ---------
wasora v0.5.267-g35a198e 
wasora’s an advanced suite for optimization & reactor analysis

 last commit on Fri Sep 21 06:18:36 2018 -0300
 compiled on 2019-02-15 08:43:19 by pablo@debian ( )
  GNU Scientific Library version 1.16
  SUNDIALs Library version 2.5.0
  GNU Readline version 6.3

 wasora is copyright (C) 2009-2018 jeremy theler
 licensed under GNU GPL version 3 or later.
 wasora is free software: you are free to change and redistribute it.
 There is NO WARRANTY, to the extent permitted by law.

The +Δ  is because I modified some archives in examples.


        



        
        

            
Hector Lestani
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Feb 15, 2019, 10:02:56 AM2/15/19
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    After re-compiling petsc and slepc, I get the same message about the
    makefile:

    

    fr@fr-VirtualBox ~/milonga $ ./autogen.sh

    Making clean in src

    make[1] Entering directory '/home/fr/milonga/src'

    Makefile:2319: *** missing separator. Stop.

    make[1]: Leaving directory '/home/fr/milonga/src'

    

    This is the error I had previously solved by adding tabs.

    But perhaps it is time to look for a better solution.

    

    When compiling petsc and slepc, the tests threw no errors.

    

    I don't know what to try now.

    

    Thanks for the answers received.
César Pablo Camusso
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Feb 15, 2019, 11:13:38 AM2/15/19
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Did you do git status?
Try rm Makefile before the ./autogen.sh

The git status is because you could have changed some file, it should appear.
The rm Makefile is because I do not have Makefile: 
pablo@debian:~/petsc/wasora-suite/milonga$ ls
AUTHORS  autoclean.sh  autogen.sh  configure.ac  COPYING  doc  examples  get.m4  INSTALL.md  locateruntest.sh  Makefile.am  NEWS  plugin.mk  PLUGINS  README.md  src  TODO  wasora




        
        

            
jeremy theler
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Feb 15, 2019, 1:07:36 PM2/15/19
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clone the milonga repository in a new location, it seems some of the manual changes persist

are the PETSC_DIR SLEPC_DIR and PETSC_ARCH correctly set? 

maybe you can even create a new temporary user and start fresh

give us all the commands you type and the output you get
also share your configure.log if you manage to get to that point

Alexis Weir
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Feb 15, 2019, 1:29:53 PM2/15/19
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Hello everyone, in milonga/autogen.sh I
      changed line 42 

    

    


    

    
undefine DESTDIR  # this variable is
      set by petsc somewhere and we need it empty to make install

    

    


    

    
with 

    

    


    

    
undefine: DESTDIR  # this variable is
      set by petsc somewhere and we need it empty to make install

    


    

    
(added colon to undefine) and this
      worked for me. Now the details

    


    

    
This is a virtualbox machine with linux
      mint 17.3 rosa (ubuntu trusty equivalent)

    
I have followed milonga instructions at
      https://www.seamplex.com/milonga/#quick-start

    
For this particular linux version some
      packages are no exactly as showed, for instance put 

    

    
sudo apt search petsc

      and you will find that the packaged needed is petsc3.4.2-dev, BUT
      as milonga request version 3.6 or newer, so I installed it from
      petsc (and slepc) web page

    
    
    
Then installing milonga  I got and
      error of missing separator in milonga/src/Makefile, and this line
      was generated by autogen.sh. Added the colon and worked

    
Perhaps in newer versions of linux this
      is not an issue, I did not check

    

    
May I generate an issue?

    
Hope this helps

    


    

    


    

    
                    Alexis

    
jeremy theler
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Feb 15, 2019, 1:43:49 PM2/15/19
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ok, I would have to take a look but after a quick look from my phone it seems that trusty is from 2014

it makes no sense to give particular instructions on the webpage on how to build on a 5 year old version

the solution for this issue and many others is:

update your operating systems!
 

jeremy theler
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Feb 15, 2019, 1:44:33 PM2/15/19
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the makefiles are generated by autoconf and friends, they are gitignored


To view this discussion on the web visit https://groups.google.com/a/seamplex.com/d/msgid/wasora/1390322555.145895.1550247200152%40mail.yahoo.com.


For more options, visit https://groups.google.com/a/seamplex.com/d/optout.


Hector Lestani
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Feb 15, 2019, 2:24:38 PM2/15/19
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    Thank you very much Alexis, and Germán, and Pablo.

    

    Now its running :) :) :)
Jeremy Theler
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Feb 16, 2019, 5:49:52 AM2/16/19
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ok, I think I understand what is going on...

Apparently the "undefine" keyword is only supported by GNU Make > 3.82

Can you people check which version of Make your Linux Mint Rosa use? Note that 3.82 is from 2010 according to the GNU Make page:



So when Alexis added a colon, instead of having the instruction "undefine DESTDIR" he added a new target which is never used, so it was like commenting out that line.

I now changed undefine to unexport which seems to be supported by the old GNU Make:



Please update to this revision and check that it works both in the old and new GNU/Linux boxes.


Regards
--
jeremy theler
César Pablo Camusso
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Feb 18, 2019, 6:34:23 AM2/18/19
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The new Makefile worked for me.

        



        
        

            
Jeremy Theler
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Feb 18, 2019, 6:42:22 AM2/18/19
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The unexport instruction appartently does not do exactly what the undefine instruction does
The make install step fails if using unexport, because it appends /usr/local/bin to DESTDIR which is something related to PETSc

I think I will switch back to undefine and support reasonable-modern OSes which can make install milonga and fino
jeremy theler
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Feb 20, 2019, 1:58:36 PM2/20/19
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any feedback on the version of make on this linux mint rosa?
Alexis Weir
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Feb 20, 2019, 2:07:04 PM2/20/19
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  GNU Make 3.81

    


    

    
almost there : D

    
Hector Lestani
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Feb 20, 2019, 2:17:48 PM2/20/19
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    Germán,

    I apologize for the lack of response. I can't turn that machine on
    right now. But I will let you know as soon as possible.

    

    Thank you.
Jeremy Theler
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Feb 21, 2019, 6:47:26 AM2/21/19
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Hector Lestani
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Feb 26, 2019, 9:28:32 AM2/26/19
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    Germán,

    the GNU Make version is 3.81 in the virtual machine, now I see that
    Alexis answered this before, as we were working on the same virtual
    machine for the students. 

    

    My question is, what would be wrong if you don't "undefine" DESTDIR
    in the Makefile? Is this a preparation for the next step of
    installation? (make install)

    

    The reason is that a virtual machine has already been distributed to
    the students (9 days ago) and it is not simple  to reinstall
    something in N machines now.

    

    In this virtual machine there was already an installation of
    milonga, so there are symlinks pointing to the right places.

    And milonga check runs perfectly all 3 test cases.

    

    I think there is no need to reinstall all the machines, right?

    

    Thanks.
jeremy theler
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Feb 27, 2019, 6:00:56 AM2/27/19
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On Tue, 2019-02-26 at 11:25 -0300, Hector Lestani wrote:



> the GNU Make version is 3.81 in the virtual machine, now I see that

> Alexis answered this before, as we were working on the same virtual

> machine for the students. 



ok, this is almost 10 years old



> My question is, what would be wrong if you don't "undefine" DESTDIR

> in the Makefile? Is this a preparation for the next step of

> installation? (make install)



yes, it is only needed to do "make install" as root and put the binary

in /usr/local/bin or wherever suitable 



> The reason is that a virtual machine has already been distributed to

> the students (9 days ago) and it is not simple  to reinstall

> something in N machines now.



> 

> In this virtual machine there was already an installation of milonga,

> so there are symlinks pointing to the right places.

> And milonga check runs perfectly all 3 test cases.

> 

> I think there is no need to reinstall all the machines, right?



no, if you copied or symlinked the binaries to a PATH directory then

you are fine.





a side question: is it really necessary to distribute milonga in a

virtual machine?



 1. in any decently-new distribution, a couple of "apt-gets" plus

"configure & make" get you going

 2. for sure something similar can be done in MacOS for those who like

to spend a lot of USD whilst giving away their freedom

 3. if the virtual machine is distributed because it contains another

piece of engineering software which is difficult to install, I would

disregard such piece of engineering software as a teaching tool

 4. if the virtual machine is distributed because students do not know

how to install GNU/Linux, then I would not give any engineering degree

to such student (seriously)



in any case, a far superior approach would be to have all the

engineering software running in a server which the students may access

through ssh with their laptops (assuming that is the current approach).

Servers usually have several gigabytes of memory and use SSD for

storage. 



actually the best scenario would be something like we had when we were

students, remember "egipcias" and "la salita"? sniff...

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> > > > > > https://groups.google.com/a/seamplex.com/d/msgid/wasora/1999149542.901120.1550489345635%40mail.yahoo.com

> > > > > > .

> > > > > > For more options, visit 

> > > > > > https://groups.google.com/a/seamplex.com/d/optout.

> > > > 

> > > > -- 

> > > > --

> > > > jeremy theler

> > > > www.seamplex.com

> > > > -- 

> > > > You received this message because you are subscribed to the

> > > > Google Groups "wasora" group.

> > > > To unsubscribe from this group and stop receiving emails from

> > > > it, send an email to wasora+un...@seamplex.com.

> > > > To post to this group, send email to was...@seamplex.com.

> > > > Visit this group at 

> > > > https://groups.google.com/a/seamplex.com/group/wasora/.

> > > > To view this discussion on the web visit 

> > > > https://groups.google.com/a/seamplex.com/d/msgid/wasora/CAK0Liyn2ejd_MTOJODsubVfauB3YnsTagyLh6784J0q%3DKbgfLw%40mail.gmail.com

> > > > .

> > > > For more options, visit 

> > > > https://groups.google.com/a/seamplex.com/d/optout.

> > > 

> > > -- 

> > > You received this message because you are subscribed to the

> > > Google Groups "wasora" group.

> > > To unsubscribe from this group and stop receiving emails from it,

> > > send an email to wasora+un...@seamplex.com.

> > > To post to this group, send email to was...@seamplex.com.

> > > Visit this group at 

> > > https://groups.google.com/a/seamplex.com/group/wasora/.

> > > To view this discussion on the web visit 

> > > https://groups.google.com/a/seamplex.com/d/msgid/wasora/ea2032b8-b471-cd4f-9f24-2ef61f0a1abf%40cab.cnea.gov.ar

> > > .

> > > For more options, visit 

> > > https://groups.google.com/a/seamplex.com/d/optout.

> >  -- 

> > You received this message because you are subscribed to the Google

> > Groups "wasora" group.

> > To unsubscribe from this group and stop receiving emails from it,

> > send an email to wasora+un...@seamplex.com.

> > To post to this group, send email to was...@seamplex.com.

> > Visit this group at 

> > https://groups.google.com/a/seamplex.com/group/wasora/.

> > To view this discussion on the web visit 

> > https://groups.google.com/a/seamplex.com/d/msgid/wasora/1550749633.3135.4.camel%40seamplex.com

> > .

> > For more options, visit 

> > https://groups.google.com/a/seamplex.com/d/optout.

>  

> -- 

> You received this message because you are subscribed to the Google

> Groups "wasora" group.

> To unsubscribe from this group and stop receiving emails from it,

> send an email to wasora+un...@seamplex.com.

> To post to this group, send email to was...@seamplex.com.

> Visit this group at 

> https://groups.google.com/a/seamplex.com/group/wasora/.

> To view this discussion on the web visit 

> https://groups.google.com/a/seamplex.com/d/msgid/wasora/62668514-2be5-4e0a-9e66-0002b71cdef8%40cab.cnea.gov.ar

> .

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