Installation help

[César Bublitz]

I tried to install milonga on ubuntu by running in terminal:

sudo apt-get install curl m4 make autoconf automake gcc git libgsl0-dev wget findutils

and then

curl https://www.seamplex.com/milonga/get.sh | sh

according instructions of website https://www.seamplex.com/milonga/. After the second attempt:
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  7974  100  7974    0     0   3802      0  0:00:02  0:00:02 --:--:--  3804
0. checking pre-requisistes...ok!
1. wasora-suite subdir exists, good!
2. pulling and updating milonga repository...ok!
3. bootstrapping milonga source tree...Cloning into 'wasora'...
remote: Counting objects: 1366, done.
remote: Compressing objects: 100% (1329/1329), done.
remote: Total 1366 (delta 935), reused 176 (delta 30)
Receiving objects: 100% (1366/1366), 775.94 KiB | 263.00 KiB/s, done.
Resolving deltas: 100% (935/935), done.
Checking connectivity... done.
fmt: 

Could not open '/PLUGINS.md' to read: File or directory not found

configure.ac:17: installing './compile'
configure.ac:17: installing './install-sh'
configure.ac:17: installing './missing'
parallel-tests: installing './test-driver'
src/Makefile.am: installing './depcomp'
ok!
4. checking for GSL...already installed!
4.5. checking for PETSc...4.5. checking for SLEPc...5. configuring milonga...configure: WARNING: sundials ida headers not found
configure: WARNING: sundials ida headers not found
configure: WARNING: sundials ida library (libsundials-ida) not found
configure: WARNING: sundials ida headers not found
configure: WARNING: sundials nvecserial library (libsundials-nvecserial) not found
configure: WARNING: GNU readline headers (libreadline-dev) not found.
configure: WARNING: GNU readline library (libreadline) not found.
configure: error: cannot find /home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4/arch-linux2-c-opt/lib/petsc/conf/petscvariables
(did you upgrade to PETSC 3.6.0?)
ok!
6. compiling milonga...make: *** 
No target indicated and no make file found. Stop.ok!
7. linking /home/cesarb/bin/milonga to the recently compiled binary...ok!
8. directory /home/cesarb/bin is already in the PATH envar, good!

something went wrong as milonga does not run :-(
share your get.log file with the mailing list for help.
see <https://groups.google.com/a/seamplex.com/forum/#!forum/wasora>

Can anyone help me?
Thank you.

[Jeremy Theler]

I don't like this line:

configure: error: cannot find /home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4/arch-linux2-c-opt/lib/petsc/conf/petscvariables

a. can you share your get.log?

b. what is the output of

$ echo $PETSC_DIR

?

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[César Bublitz]

Hi. Thank you for the answer.

a. I shared the get.log file.
b. The output is

/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4

[Jeremy Theler]

there is something wrong with the configuration of PETSc, but we'll go step by step and maybe other people from the list can also benefit also

so now let's try to do

$ cd $PETSC_DIR

$ ./configure --download-cblaslapack --with-mpi=0 --with-debugging=0

and tell us what happens

[César Pablo Camusso]

Dear César,

I think you forgot to install sundials and readline.

To install sundials:

apt-get install libsundial*

To install readline:

apt-get install libreadline libreadline-dev

You can read the "no" in get.log. For example the line:

checking sundials/sundials_types.h usability... no

means that sundials is not installed.

I do not know the meaning of the last line:

checking for PETSc arch... broken

Perhaps PETSc is not correctly installed.

Once it is ready, try to install milonga again.

El miércoles, 28 de marzo de 2018 09:07:01 ART, César Bublitz <cesa...@gmail.com> escribió:

Hi. Thank you for the answer.

a. I shared the get.log file.
b. The output is

/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4



Em quarta-feira, 28 de março de 2018 06:47:47 UTC-3, Jeremy escreveu:

I don't like this line:

configure: error: cannot find /home/cesarb/wasora-suite/ milonga/libs/petsc-3.7.4/arch- linux2-c-opt/lib/petsc/conf/ petscvariables

a. can you share your get.log?

b. what is the output of

$ echo $PETSC_DIR

?

On Tue, 2018-03-27 at 19:54 -0700, César Bublitz wrote:

I tried to install milonga on ubuntu by running in terminal:

sudo apt-get install curl m4 make autoconf automake gcc git libgsl0-dev wget findutils

and then

curl https://www.seamplex.com/ milonga/get.sh | sh

according instructions of website https://www.seamplex.com/ milonga/. After the second attempt:

To view this discussion on the web visit https://groups.google.com/a/seamplex.com/d/msgid/wasora/61fae070-5ae7-4173-81f2-882cecdd0e52%40seamplex.com.

[jeremy theler]

SUNDIALS and Readline are optional, they are not mentioned in the get.sh script

The first one only makes sense in wasora in order to solve DAEs

The second one liny makes sense if you want to enter "debug-mode" and do step-by-step advancements

In principle they are not needed for milonga unless you want to solve strange things like mixing DAEs with steady-state computations or use your kinematics branch

To view this discussion on the web visit https://groups.google.com/a/seamplex.com/d/msgid/wasora/1842602144.232122.1522240922357%40mail.yahoo.com.

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

--

--

jeremy theler

www.seamplex.com

[César Bublitz]

Following your suggestion, the result was

Configuring PETSc to compile on your system

===============================================================================

=============================================================================== ***** WARNING: Using default optimization C flags -g -O You might consider manually setting optimal optimization flags for your system with COPTFLAGS="optimization flags" see config/examples/arch-*-opt.py for examples =============================================================================== =============================================================================== ***** WARNING: Using default C++ optimization flags -g -O You might consider manually setting optimal optimization flags for your system with CXXOPTFLAGS="optimization flags" see config/examples/arch-*-opt.py for examples =============================================================================== =============================================================================== ***** WARNING: Using default FORTRAN optimization flags -g -O You might consider manually setting optimal optimization flags for your system with FOPTFLAGS="optimization flags" see config/examples/arch-*-opt.py for examples =============================================================================== =============================================================================== WARNING! Compiling PETSc with no debugging, this should only be done for timing and production runs. All development should be done when configured using --with-debugging=1 =============================================================================== =============================================================================== It appears you do not have valgrind installed on your system. We HIGHLY recommend you install it from www.valgrind.org Or install valgrind-devel or equivalent using your package manager. Then rerun ./configure =============================================================================== Compilers:

C Compiler: gcc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O

C++ Compiler: g++ -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O -fPIC

Fortran Compiler: gfortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O

Linkers:

Shared linker: gcc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O

Dynamic linker: gcc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O

make:

BLAS/LAPACK: -llapack -lblas

Arch:

pthread:

Library: -lpthread

PETSc:

PETSC_ARCH: arch-linux2-c-opt

PETSC_DIR: /home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4

Scalar type: real

Precision: double

Clanguage: C

shared libraries: enabled

Integer size: 32

Memory alignment: 16

xxx=========================================================================xxx

Configure stage complete. Now build PETSc libraries with (gnumake build):

make PETSC_DIR=/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4 PETSC_ARCH=arch-linux2-c-opt all

xxx=========================================================================xxx

But "make" command don't work. Then, I installed valgrind package and run again

$ curl https://www.seamplex.com/milonga/get.sh | sh

which didn't work again. Finally, I re-run

$ cd $PETSC_DIR

$ ./configure --download-cblaslapack --with-mpi=0 --with-debugging=0

 

and it works.

Thanks a lot for the help!

[jeremy theler]

I would like to know why the make step failed, did you save the error message so we can share the findings with other people?

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[César]

I'm sorry for bothering you again. As a beginner Linux user, I understand that I need to study more about it. But I could not solve the problem because I can not find the binary file. In the home/bin directory, there is a link to the /wasora-suite/milonga directory that leads to the milonga file that does not exist.

Did I have a problem with the installation or is it ignorance of me?

After test performed:

cesarb@cesarb-Presario-CQ43-Notebook-PC:~/wasora-suite/milonga/libs/petsc-3.7.4$ make PETSC_DIR=/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4 PETSC_ARCH=arch-linux2-c-opt test
Running test examples to verify correct installation
Using PETSC_DIR=/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4 and PETSC_ARCH=arch-linux2-c-opt
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process
Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process
Completed test examples
=========================================
Now to evaluate the computer systems you plan use - do:
make PETSC_DIR=/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4 PETSC_ARCH=arch-linux2-c-opt streams

cesarb@cesarb-Presario-CQ43-Notebook-PC:~/wasora-suite/milonga/libs/petsc-3.7.4$ make PETSC_DIR=/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4 PETSC_ARCH=arch-linux2-c-opt streams
cd src/benchmarks/streams; /usr/bin/make --no-print-directory PETSC_DIR=/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4 PETSC_ARCH=arch-linux2-c-opt streams
gcc -o MPIVersion.o -c -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O -I/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4/include -I/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4/arch-linux2-c-opt/include -I/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4/include/petsc/mpiuni `pwd`/MPIVersion.c
Running streams with '/home/cesarb/wasora-suite/milonga/libs/petsc-3.7.4/bin/petsc-mpiexec.uni ' using 'NPMAX=4'
Number of MPI processes 1 Processor names localhost
Triad: 10071.3653 Rate (MB/s)
Uniprocessor version of MPI can only use one processor
Uniprocessor version of MPI can only use one processor
Uniprocessor version of MPI can only use one processor
------------------------------------------------

cesarb@cesarb-Presario-CQ43-Notebook-PC:~/wasora-suite/milonga/libs/petsc-3.7.4$ cd

cesarb@cesarb-Presario-CQ43-Notebook-PC:~$ cd wasora-suite/milonga/examples

cesarb@cesarb-Presario-CQ43-Notebook-PC:~/wasora-suite/milonga/examples$ milonga slab.mil
milonga: command not found

Thank you.

[Vitor Vasconcelos]

Probably milonga is not in your $PATH.
You must refer to its full path (or relative path)

try: ../milonga slab.mil (from examples dir)
or: ~/wasora-suite/milonga/milonga slab.mil (from examples dir)

Vitor

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[jeremy theler]

did you actually compile milonga or just PESTc/SLEPc?

the usual steps are
cd to milonga path
./autogen.sh
./configure
make
make check

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[jeremy theler]

ok I am not able to follow and I do not know what you are referring to

does anybody else here can help him?

On Fri, Mar 30, 2018, 17:34 César Bublitz <cesa...@gmail.com> wrote:

Hi,

The final "make" command works (after the steps mentioned in the previous message). When it didn't work, the message was that make file was not found:

To view this discussion on the web visit https://groups.google.com/a/seamplex.com/d/msgid/wasora/d8885436-466e-42ac-8881-901aee337410%40seamplex.com.

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[jeremy theler]

so, to straighten things up

I assume you already have a working PETSc/SLEPc version

so, type each of these lines from scratch and tell us what error gives each one of them

cd $HOME

mkdir wasora-suite

cd wasora-suite

git clone https://bitbucket.org/seamplex/wasora.git
cd wasora

./autogen.sh

./configure

make

make check

cd ..

git clone https://bitbucket.org/seamplex/milonga.git

./autogen.sh

./configure

make

make check

cd ..

[jeremy theler]

sorry, ther's a missing "cd milonga" after cloning milonga

if the repositories are already cloned, then cd to them and do "git pull" to refresh