installation problems on mac  [SOLVED]

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maths
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Joined: Tue Oct 13, 2015 6:15 pm

installation problems on mac  [SOLVED]

Post by maths » Wed Oct 14, 2015 4:22 pm

Hello,
I try to install abinit on my mac for two days without success :o. I can easily ./configure. After its done --You may now type "make" to build ABINIT.-- appears, but if I type make. the following ERROR massage appears:

Code: Select all

/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
Making all in fallbacks
/Applications/Xcode.app/Contents/Developer/usr/bin/make fox
The build of fox has been disabled
touch: stamps/fox-install-stamp: No such file or directory
make[3]: *** [fox] Error 1
make[2]: [all-local] Error 2 (ignored)
Checking build of fox fallback
test -e stamps/fox-install-stamp
make[2]: *** [all-local] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2


now i don't know what to do. I am unfortunately not 100% familiar to the terminal commands (I just know a few basics). So pleas help me but speak an easy language :).
lg matt

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jbeuken
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Re: installation problems on mac

Post by jbeuken » Wed Oct 14, 2015 10:07 pm

Hi,

did you read the content of the README.MacOSX file found in the root of source tree of 7.10.4 version ?

jmb
------
Jean-Michel Beuken
Computer Scientist

maths
Posts: 23
Joined: Tue Oct 13, 2015 6:15 pm

Re: installation problems on mac

Post by maths » Thu Oct 15, 2015 3:43 pm

Hi,
I can not fined a README.MacOSX file in abinit-7.10.4!?
I followed the instruction on the web page. I tried also to create a tmp directory and ../configure and then it installed I think, but make test_fast didn`t work
then I deleted it and cofigurate it new and now I am again not able to install it via make.
matt

maths
Posts: 23
Joined: Tue Oct 13, 2015 6:15 pm

Re: installation problems on mac

Post by maths » Thu Oct 15, 2015 5:58 pm

New status!
I again installed de fortran g77 compiler.
I dragged the abinit-xxx directory into Applications.
Via terminal I (created a temp) mkdir temp, where I plugged in ../configure. After it was done, I typed make and it showed:

Code: Select all

==============================================================================
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
Making install in tests
==============================================================================
Use the script  runtests.py  for a flexible use of the test suite.
To get help, issue                   ./runtests.py --help | more

To run the new test suite inside a tmp directory (e.g. ~abinit/tmp/tests) :
../../tests/runtests.py
this will create a directory tmp/tests/Test_suite
Useful option when using manually the test suite : "-t0"
   (which disable the timeout routine)

Keywords to use with the make command for test directory (automated sets of tests) :

check_local    Standard set of tests, used on the test farm slaves
tests_abirules Launch the abirules tests
               (Warning : for some of the tests, the file make.log
                must be present in the top directory. This means one has
                to compile with the command   make > make.log 2>&1 )
tests_buildsys Launch the buildsys tests
tests_in       Launch several small tests (3 mandatory ones, for basic
               capabilities of ABINIT, and 4 optional, to test
               bigdft, etsf_io, libxc, wannier90, if they are installed)

One should check whether the following keywords still work :
benchabinit
tests_bench    Test accuracy+cpu for benchmarks (with a report)
tests_speed    Test cpu for benchmarks (quick, with a report)

To add a new test, see
http://www.abinit.org/developers/dev-environment/buildbot/howto-add-a-new-test-in-the-test-suite

==============================================================================
make[3]: Nothing to be done for `install-exec-am'.


Then I also did make install.
Finally i tried this make test_fast in /Applications/abinit-7.10.4/tmp/src/98_main. But:

Code: Select all

make: *** No rule to make target `test_fast'.  Stop.

what to do??? :cry:

PS:
I also tried it with home-brew. Explained hier https://wiki.abinit.org/doku.php?id=tips:howto_macosx. I took nearly 1h. The problem is it created a /usr/local/Cellar/abinit/7.10.4_1 but no 98_main or anything where I can work ... i don't really know what it did?
greets matt

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jbeuken
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Re: installation problems on mac

Post by jbeuken » Thu Oct 15, 2015 8:01 pm

Argh !

you are right ! it is in version 7.10.5 ( not published ) :(
find a version of README.MacOSX attached...

I again installed de fortran g77 compiler.


:shock: I don't understand :roll:
we use, at minimum, Fortran 95 and part of Fortran 2003
Fortran 77 can no longer compile ABINIT… ;)

Sorry,

jmb
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README.MacOSX.log
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Jean-Michel Beuken
Computer Scientist

maths
Posts: 23
Joined: Tue Oct 13, 2015 6:15 pm

Re: installation problems on mac

Post by maths » Thu Oct 15, 2015 8:35 pm

Hi,
I Found the same in web see link above! I tried it with homebrew but I can't find main directory ....as mentioned :(
It's frustrating me arrr
Bg lg

maths
Posts: 23
Joined: Tue Oct 13, 2015 6:15 pm

Re: installation problems on mac

Post by maths » Fri Oct 16, 2015 9:13 pm

I tried it know with option 3- COMPILING ABINIT BY YOURSELF under MacOSX:

There I fail at the point
* Create a working directory:
cd abinit_src_dir
mkdir build && cd build
where schuld I type in cd abinit_src_dir (such a directory does not exist!!??)
argh!

plz help!
mthx

maths
Posts: 23
Joined: Tue Oct 13, 2015 6:15 pm

Re: installation problems on mac

Post by maths » Mon Oct 19, 2015 6:21 pm

If I understand the README right, i have to type:

Code: Select all

user:~$ tar -xzf Downloads/abinit-7.10.5.tar
user:~$ cd abinit-7.10.5/
user:~$ mkdir build && cd build
user:~$ ../configure FC=gfortran CC=clang FCFLAGS_EXTRA="-ffree-line-length-none"
user:~$ make mj4


also tried it with simple make
result is an error (gfortran works... I tested it with a small program):
(scroll down)

Code: Select all

/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
Making all in fallbacks
/Applications/Xcode.app/Contents/Developer/usr/bin/make fox
The build of fox has been disabled
Checking build of fox fallback
test -e stamps/fox-install-stamp
/Applications/Xcode.app/Contents/Developer/usr/bin/make libxc
The build of libxc has been disabled
Checking build of libxc fallback
test -e stamps/libxc-install-stamp
/Applications/Xcode.app/Contents/Developer/usr/bin/make linalg
The build of linalg has been disabled
Checking build of linalg fallback
test -e stamps/linalg-install-stamp
/Applications/Xcode.app/Contents/Developer/usr/bin/make netcdf
The build of netcdf has been disabled
Checking build of netcdf fallback
test -e stamps/netcdf-install-stamp
/Applications/Xcode.app/Contents/Developer/usr/bin/make atompaw
The build of atompaw has been disabled
Checking build of atompaw fallback
test -e stamps/atompaw-install-stamp
/Applications/Xcode.app/Contents/Developer/usr/bin/make etsf_io
The build of etsf_io has been disabled
Checking build of etsf_io fallback
test -e stamps/etsf_io-install-stamp
/Applications/Xcode.app/Contents/Developer/usr/bin/make wannier90
The build of wannier90 has been disabled
Checking build of wannier90 fallback
test -e stamps/wannier90-install-stamp
/Applications/Xcode.app/Contents/Developer/usr/bin/make bigdft
The build of bigdft has been disabled
Checking build of bigdft fallback
test -e stamps/bigdft-install-stamp
Making all in src
Making all in incs
There is no buildable file here
Making all in mods
There is no buildable file here
Making all in 01_linalg_ext
gfortran -DHAVE_CONFIG_H -I. -I../../../src/01_linalg_ext -I../..  -I../../src/incs -I../../../src/incs -I/Volumes/Macintosh HD/Benutzer/matthiaskehrer/abinit-7.10.5/build/fallbacks/exports/include   -ffree-form -J/Volumes/Macintosh HD/Benutzer/matthiaskehrer/abinit-7.10.5/build/src/mods -O2 -mtune=native -march=native -g -ffree-line-length-none -ffree-line-length-none  -c -o m_linalg_interfaces.o ../../../src/01_linalg_ext/m_linalg_interfaces.F90
gfortran: error: HD/Benutzer/matthiaskehrer/abinit-7.10.5/build/fallbacks/exports/include: No such file or directory
gfortran: error: HD/Benutzer/matthiaskehrer/abinit-7.10.5/build/src/mods: No such file or directory
make[3]: *** [m_linalg_interfaces.o] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error
2

plz help me!
thx very much
maths

Jordan
Posts: 282
Joined: Tue May 07, 2013 9:47 am

Re: installation problems on mac

Post by Jordan » Tue Oct 20, 2015 9:04 am

Your problem is probably the space you have between "Macintosh" and "HD".
When you have something like

Code: Select all

-I/Volumes/Macintosh HD/Benutzer/matthiaskehrer/abinit-7.10.5/build/fallbacks/exports/include

it is really understood as two different entities because of the space
In your configuration step you should try to enforce the name using Macintosh\ HD (note the \) or by using double quotes.

Or you can change your mount point from /Volumes/Macintosh HD to /Volumes/Macintosh_HD

Or you can just compile the code somewhere else to avoid this issue.

Cheers

Jordan

maths
Posts: 23
Joined: Tue Oct 13, 2015 6:15 pm

Re: installation problems on mac

Post by maths » Tue Oct 20, 2015 3:23 pm

I entered abinit now threw /Benutzer/matthiaskehrer/abinit/abinit-7.10.5
There is no space in the path. make looked good but make test_fast failed again in /Benutzer/matthiaskehrer/abinit/abinit-7.10.5/src/98_main (seems there is no such file/directory)
Result of matthiaskehrer:tests$ ./runtests.py

Code: Select all

Suite        failed  passed  succeeded  skipped  disabled  run_etime  tot_etime
atompaw           0       0          0        2         0       0.00       0.02
bigdft            0       0          0       22         0       0.00       0.01
built-in          2       0          1        4         0       4.17       4.19
etsf_io           0       0          0        7         0       0.00       0.00
fast              8       0          3        0         0      22.88      23.97
fox               0       0          0        2         0       0.00       0.00
gpu               0       0          0        4         0       0.00       0.00
libxc             0       0          0       21         0       0.00       0.01
mpiio             0       0          0       14         0       0.00       0.01
paral            20       0          1       69         0      43.10      43.88
seq              19       0          0        0         0      38.39      38.95
tutoparal         0       0          0        2         0       0.00       0.00
tutoplugs         0       0          0        4         0       0.00       0.00
tutorespfn       23       0          0        0         0      63.68      65.15
tutorial         36       1         11        0         0     117.23     119.67
unitary           0       0         17       17         0      53.83      54.37
v1               52       0         24        0         0     125.68     131.50
v2               40       0         39        0         0     183.15     189.93
v3               55       1         24        0         0     237.44     248.33
v4               44       0         18        0         0     170.28     177.90
v5               56       0         18        0         0     222.98     229.36
v6               48       0         12        0         0     167.27     172.48
v67mbpt          18       0          0        0         0      38.35      40.13
v7               32       0          1        0         0     103.66     107.44
vdwxc             0       0          0        1         0       0.00       0.00
wannier90         0       0          0        7         0       0.00       0.00


Code: Select all

/bin/sh: line 1: 49250 Segmentation fault: 11  /Benutzer/matthiaskehrer/abinit/abinit-7.10.5/build/src/98_main/abinit < /Benutzer/matthiaskehrer/abinit/abinit-7.10.5/build/tests/Test_suite/v7_t67/t67.stdin > /Benutzer/matthiaskehrer/abinit/abinit-7.10.5/build/tests/Test_suite/v7_t67/t67.stdout 2> /Benutzer/matthiaskehrer/abinit/abinit-7.10.5/build/tests/Test_suite/v7_t67/t67.stderr
Command   /Benutzer/matthiaskehrer/abinit/abinit-7.10.5/build/src/98_main/abinit < /Benutzer/matthiaskehrer/abinit/abinit-7.10.5/build/tests/Test_suite/v7_t67/t67.stdin > /Benutzer/matthiaskehrer/abinit/abinit-7.10.5/build/tests/Test_suite/v7_t67/t67.stdout 2> /Benutzer/matthiaskehrer/abinit/abinit-7.10.5/build/tests/Test_suite/v7_t67/t67.stderr
 returned exit_code: 139

[v7][t67][np=1]: fldiff.pl fatal error:
The diff analysis cannot be done: the number of lines to be analysed differ.
File /Benutzer/matthiaskehrer/abinit/abinit-7.10.5/tests/v7/Refs/t67.out: 287 lines, 36 ignored
File /Benutzer/matthiaskehrer/abinit/abinit-7.10.5/build/tests/Test_suite/v7_t67/t67.out: 286 lines, 36 ignored
[v7][t67][np=1]Test was not expected to fail but subrocesses returned 139

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x10fee7092
#1  0x10fee63b0
#2  0x7fff8d2f1529
#3  0x7fff80fc6b8e
#4  0x10beedcd2
#5  0x10beedf2c
#6  0x10b69a1db
#7  0x10b32df56
#8  0x10b338460
#9  0x10b2e40af
#10  0x10b2d2550
#11  0x10b24123f
#12  0x10b246bc3
#13  0x10b22a7e4
#14  0x10b21369c
#15  0x10bf37dbe

:(
thx for the help!
maths

Jordan
Posts: 282
Joined: Tue May 07, 2013 9:47 am

Re: installation problems on mac

Post by Jordan » Thu Oct 22, 2015 8:55 am

Thas's already a progress.

What I could suggest, is configure abinit with

Code: Select all

../configure FC=gfortran CC=clang FCFLAGS_EXTRA="-ffree-line-length-none -fbacktrace"
make distclean
make mj4


The -fbacktrace should add the subroutine, line and file in which the segfault occures.
Some tests seem to passed so it should not be a big thing.

You can also check if it comes from some special features of you cpu like avx/avx2 but disabling the optimizationss (--enable-optim=no)
See ../configure --help for compilation options.

maths
Posts: 23
Joined: Tue Oct 13, 2015 6:15 pm

Re: installation problems on mac

Post by maths » Thu Oct 22, 2015 6:37 pm

Thx for your answer!
But it didn't work:

Code: Select all

matthiaskehrer:build$ make mj4
make: *** No rule to make target `mj4'.  Stop.

after

Code: Select all

matthiaskehrer:abinit-7.10.5$ cd build/
matthiaskehrer:build$ ../configure FC=gfortran CC=clang FCFLAGS_EXTRA="-ffree-li
make distclean
make mj4


I didn't really get your other advice?
greets

maths
Posts: 23
Joined: Tue Oct 13, 2015 6:15 pm

Re: installation problems on mac

Post by maths » Fri Oct 23, 2015 12:39 pm

It works!! I tried in once more like before (following the README and avoid path Macintosh HD) and in works know.
thx very much for the help and sry for my disqualification :)
BR maths

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