make test failed

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kaushikchemhatua
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make test failed

Post by kaushikchemhatua » 19 Mar 2015, 03:06

Hi everybody may be I am asking stupid question
I install DALTON 2013 as follows
./setup --mpi
Cd build
Make
Make dalton.x
Make lsdalton.x
Make -j4
Make test

All the test failed saying that no network for out of band communication

bast
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Re: make test failed

Post by bast » 19 Mar 2015, 08:42

first of all "make" includes "make dalton.x" and "make lsdalton.x".
then to debug the MPI problem i recommend to run a single MPI calculation
to see whether this works.
also please mind that here "make test" does not know on how many MPI tasks
it should run, so please specify this:

Code: Select all

$ export DALTON_LAUNCHER="mpirun -np 8" # adapt to your situation
$ export LSDALTON_LAUNCHER="mpirun -np 8" # adapt to your situation
$ make test

taylor
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Re: make test failed

Post by taylor » 19 Mar 2015, 08:59

Can I also add a question following Radovan's post? If you setup and build without invoking MPI, does the resulting code run the tests? If it does, the problem (and this comes up frequently) may very well be with the MPI installation that you are linking against. If the tests don't run even with the most basic build of the code (no MPI, no OpenMP), then there is a problem with how you are building it (I am not suggesting that's necessarily your fault, it may be an intrinsic Dalton problem!) and that is what we need to investigate.

I make this point because if it is a Dalton problem, we should be able to help directly by e.g. looking at log files you post, and so forth. But if it is an MPI problem, it is more likely that you will have to turn to local system administrators, or yourself if you are the sysadmin, for assistance. We may be able to offer some suggestions, but if it is a local problem that's probably all we can do.

Best regards
Pete

kaushikchemhatua
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Re: make test failed

Post by kaushikchemhatua » 19 Mar 2015, 17:21

Yes indeed Dalton has been compiled without mpi and everything is fine. I recently install mpi for my Desktop and go for parallel execution. Following command has been tested
Which mpif90, which mpicc, which mpicxx has been used and found ok.
Setup command, setup_make_output and last temp log file has been attached
Attachments
setu-_make.zip
(6.47 KiB) Downloaded 465 times

bast
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Re: make test failed

Post by bast » 19 Mar 2015, 17:28

kaushikchemhatua wrote:Yes indeed Dalton has been compiled without mpi and everything is fine. I recently install mpi for my Desktop and go for parallel execution. Following command has been tested
Which mpif90, which mpicc, which mpicxx has been used and found ok.
Setup command, setup_make_output and last temp log file has been attached
i don't think this problem is related to Dalton.
i recommend to download a hello world MPI program, for instance from here:
https://www.nersc.gov/users/computation ... g-started/
(but there are countless sources on the net).
then compile it and try to run it:

Code: Select all

$ mpif90 -o hello.x hello.F90
$ /usr/local/bin/mpiexec -np 4 ./hello.x
does this work?
also check that the mpiexec that you use there is the one
you actually installed.

vlado
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Re: make test failed

Post by vlado » 08 Jun 2015, 10:15

Hello everyone,
I may have a similar problem with the 'make' step of the installation of Dalton 2015. I am trying a serial installation (no MPI).
The 'setup' step seems to be OK, i used:

Code: Select all

./setup --fc=gfortran --cc=gcc --cxx=g++ --blas=none --lapack=none --explicit-libs="-L/home/vlado/PROG/lib/atlas/lib -llapack -lcblas -latlas -lf77blas" build_gfortran
Then the obvious cd to build_gfortran, and then make, which did:

Code: Select all

Scanning dependencies of target check_external_timestamp_qfitlib
[  0%] Built target check_external_timestamp_qfitlib
Scanning dependencies of target check_external_timestamp_gen1int
[  0%] Built target check_external_timestamp_gen1int
Scanning dependencies of target gen1int
[  0%] Creating directories for 'gen1int'
[  0%] Performing download step for 'gen1int'

[  0%] No patch step for 'gen1int'
[  0%] No update step for 'gen1int'
[  0%] Performing configure step for 'gen1int'
-- The C compiler identification is GNU 4.1.2
-- The Fortran compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Configuring done
-- Generating done
-- Build files have been written to: /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build
[  0%] Performing build step for 'gen1int'
Scanning dependencies of target gen1int
[  0%] Building Fortran object CMakeFiles/gen1int.dir/src/xkind.F90.o
[  1%] Building Fortran object CMakeFiles/gen1int.dir/src/london_ao.F90.o
 In file /home/vlado/PROG/DALTON/DALTON-Source/external/gen1int/src/london_ao.F90:25

  use xkind
          1
Fatal Error: Can't open module file 'xkind.mod' for reading at (1): No such file or directory
make[6]: *** [CMakeFiles/gen1int.dir/src/london_ao.F90.o] Error 1
make[5]: *** [CMakeFiles/gen1int.dir/src/london_ao.F90.o.provides] Error 2
make[4]: *** [CMakeFiles/gen1int.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [external/gen1int-stamp/gen1int-build] Error 2
make[1]: *** [gen1int/CMakeFiles/gen1int.dir/all] Error 2
make: *** [all] Error 2
So what could have possibly gone wrong? Or better yet, why is there no 'xkind.mod' for reading? And most importantly, does anyone know a solution to this problem?
I used cmake-3.2, it is a CentOS 5.11 desktop computer...

Any help appreciated, thank you in advance!
Regards,
Vlado

gaobin
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Re: make test failed

Post by gaobin » 08 Jun 2015, 13:26

Hi Vlado,

I would suggest that you try "make VERBOSE=1" to show you the full compiling commands, and then you post these commands here.

In your case, all the module files will be generated in build_gfortran/modules, your compiler should include this directory in the compiling commands. Otherwise, you will have the "no mod" problem.

Cheers
Gao

vlado
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Re: make test failed

Post by vlado » 08 Jun 2015, 13:44

OK, thanks. So I tried 'make VERBOSE=1' and the output got more detailed (the VERBOSE=1 invokes just that it makes a "debugging" output?):

Code: Select all

/usr/local/bin/cmake -H/home/vlado/PROG/DALTON/DALTON-Source -B/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/bin/cmake -E cmake_progress_start /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/CMakeFiles /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
make -f CMakeFiles/check_external_timestamp_qfitlib.dir/build.make CMakeFiles/check_external_timestamp_qfitlib.dir/depend
make[2]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
cd /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /home/vlado/PROG/DALTON/DALTON-Source /home/vlado/PROG/DALTON/DALTON-Source /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/CMakeFiles/check_external_timestamp_qfitlib.dir/DependInfo.cmake --color=
make[2]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
make -f CMakeFiles/check_external_timestamp_qfitlib.dir/build.make CMakeFiles/check_external_timestamp_qfitlib.dir/build
make[2]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
python /home/vlado/PROG/DALTON/DALTON-Source/cmake/check_external_timestamp.py /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/qfitlib-stamp/qfitlib-configure /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/qfitlib-stamp /home/vlado/PROG/DALTON/DALTON-Source/external/qfitlib
make[2]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
/usr/local/bin/cmake -E cmake_progress_report /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/CMakeFiles
[  0%] Built target check_external_timestamp_qfitlib
make -f gen1int/CMakeFiles/check_external_timestamp_gen1int.dir/build.make gen1int/CMakeFiles/check_external_timestamp_gen1int.dir/depend
make[2]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
cd /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /home/vlado/PROG/DALTON/DALTON-Source /home/vlado/PROG/DALTON/DALTON-Source/DALTON/gen1int /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/gen1int /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/gen1int/CMakeFiles/check_external_timestamp_gen1int.dir/DependInfo.cmake --color=
make[2]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
make -f gen1int/CMakeFiles/check_external_timestamp_gen1int.dir/build.make gen1int/CMakeFiles/check_external_timestamp_gen1int.dir/build
make[2]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
cd /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/gen1int && python /home/vlado/PROG/DALTON/DALTON-Source/cmake/check_external_timestamp.py /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-stamp/gen1int-configure /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-stamp /home/vlado/PROG/DALTON/DALTON-Source/external/gen1int
make[2]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
/usr/local/bin/cmake -E cmake_progress_report /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/CMakeFiles
[  0%] Built target check_external_timestamp_gen1int
make -f gen1int/CMakeFiles/gen1int.dir/build.make gen1int/CMakeFiles/gen1int.dir/depend
make[2]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
cd /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /home/vlado/PROG/DALTON/DALTON-Source /home/vlado/PROG/DALTON/DALTON-Source/DALTON/gen1int /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/gen1int /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/gen1int/CMakeFiles/gen1int.dir/DependInfo.cmake --color=
make[2]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
make -f gen1int/CMakeFiles/gen1int.dir/build.make gen1int/CMakeFiles/gen1int.dir/build
make[2]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
/usr/local/bin/cmake -E cmake_progress_report /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/CMakeFiles
[  0%] Performing build step for 'gen1int'
cd /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build && make
make[3]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
/usr/local/bin/cmake -H/home/vlado/PROG/DALTON/DALTON-Source/external/gen1int -B/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/bin/cmake -E cmake_progress_start /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build/CMakeFiles /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[4]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
make -f CMakeFiles/gen1int.dir/build.make CMakeFiles/gen1int.dir/depend
make[5]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
cd /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /home/vlado/PROG/DALTON/DALTON-Source/external/gen1int /home/vlado/PROG/DALTON/DALTON-Source/external/gen1int /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build/CMakeFiles/gen1int.dir/DependInfo.cmake --color=
make[5]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
make -f CMakeFiles/gen1int.dir/build.make CMakeFiles/gen1int.dir/requires
make[5]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
make -f CMakeFiles/gen1int.dir/build.make CMakeFiles/gen1int.dir/src/xkind.F90.o.provides.build
make[6]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
make[6]: `CMakeFiles/gen1int.dir/src/xkind.F90.o.provides.build' is up to date.
make[6]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
make -f CMakeFiles/gen1int.dir/build.make CMakeFiles/gen1int.dir/src/london_ao.F90.o.provides.build
make[6]: Entering directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
/usr/local/bin/cmake -E cmake_progress_report /home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build/CMakeFiles 47
[  1%] Building Fortran object CMakeFiles/gen1int.dir/src/london_ao.F90.o
/usr/bin/gfortran  -DBUILD_F90_MODULE -m64 -O3 -J/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/modules -I/home/vlado/PROG/DALTON/DALTON-Source/external/gen1int/include    -c /home/vlado/PROG/DALTON/DALTON-Source/external/gen1int/src/london_ao.F90 -o CMakeFiles/gen1int.dir/src/london_ao.F90.o
 In file /home/vlado/PROG/DALTON/DALTON-Source/external/gen1int/src/london_ao.F90:25

  use xkind
          1
Fatal Error: Can't open module file 'xkind.mod' for reading at (1): No such file or directory
make[6]: *** [CMakeFiles/gen1int.dir/src/london_ao.F90.o] Error 1
make[6]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
make[5]: *** [CMakeFiles/gen1int.dir/src/london_ao.F90.o.provides] Error 2
make[5]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
make[4]: *** [CMakeFiles/gen1int.dir/all] Error 2
make[4]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
make[3]: *** [all] Error 2
make[3]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/gen1int-build'
make[2]: *** [external/gen1int-stamp/gen1int-build] Error 2
make[2]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
make[1]: *** [gen1int/CMakeFiles/gen1int.dir/all] Error 2
make[1]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
make: *** [all] Error 2
I can't identify the source of the problem... I did just that, i.e. 'make VERBOSE=1' with the old "output" from the setup script (i.e. setup wasn't run again). Sorry for my ignorance, but how do I know if the compiler does include the modules in build_gfortran/modules in the compilation (how to set it so it does include it)? Because the build_gfortran/modules directory contains (so far) just that one file xkind.mod file...

But thank you a lot for the suggestion.
Regards,
Vlado
Last edited by vlado on 08 Jun 2015, 13:50, edited 1 time in total.

gaobin
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Country: Norway

Re: make test failed

Post by gaobin » 08 Jun 2015, 13:49

Hi Vlado,

I am not an expert of gfortran, but I guess "-J/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/modules" should include this module path. Could you please check if you have xkind.mod in this directory (/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/modules)? If not, then the problem is xkind.F90 is not successfully compiled. You need to check why. But if you have xkind.mod, this will be related to gfortran compiler, why it can not include this module path? Hope other guys on this forum can answer these.

Cheers
Gao

vlado
Posts: 7
Joined: 08 Jun 2015, 07:52
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Last name(s): Sladek
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Country: Slovakia

Re: make test failed

Post by vlado » 08 Jun 2015, 14:02

yes the xkind.mod file is where it should be. But the compiler seems not to take the flag "-J/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/modules"
But when is it appropriate to give this command? In the ./setup -other-flags "-J/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/modules" (with/without quotes) or to the make script? Anyway, neither one takes it in this form. Will try to google the proper syntax...
Thank you Gao.
regards,
Vlado

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magnus
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Re: make test failed

Post by magnus » 08 Jun 2015, 14:11

It is most likely because you are using an old gcc (4.1.2). I believe Dalton requires >= 4.4. GCC version 4.4 is often available as gcc44 (and gfortran44 and g++44) on older CentOSs.

vlado
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Re: make test failed

Post by vlado » 08 Jun 2015, 14:55

Thanks, the commands:

./setup --fc=gfortran44 --cc=gcc44 --cxx=g++44 --blas=none --lapack=none --explicit-libs="-L/home/vlado/PROG/lib/atlas/lib -llapack -lcblas -latlas -lf77blas" build_gfortran

and

make -I/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/modules VERBOSE=1

seem to have fixed the "module" issue (so it's -I for gfortran...), but now it reports something else at 65% (make went 2 times relatively quickly to 100% and then once slowly to 65% and finished with the following, which I guess is not the correct finish):

Code: Select all

Linking Fortran executable dalton.x
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/dalton.x.dir/link.txt --verbose=1
/usr/bin/gfortran44    -DVAR_GFORTRAN -DGFORTRAN=445 -ffloat-store -fcray-pointer -m64 -w -O3 -ffast-math -funroll-loops -ftree-vectorize CMakeFiles/dalton.x.dir/DALTON/abacus/dalton.F.o  -o dalton.x  -L/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/lib  -L/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/pelib-build/external/lib  -L/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/qfitlib-build/external/lib -rdynamic lib/libdalton.a external/lib/libqfitlib.a external/lib/libpelib.a lib/libgen1int_interface.a external/lib/libgen1int.a -L/home/vlado/PROG/lib/atlas/lib -llapack -lcblas -latlas -lf77blas -Wl,-rpath,/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/lib:/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/pelib-build/external/lib:/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran/external/qfitlib-build/external/lib:
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_dasum.o): In function `atl_f77wrap_dasum_':
ATL_F77wrap_asum.c:(.text+0x12): undefined reference to `ATL_dasum'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_drot.o): In function `atl_f77wrap_drot_':
ATL_F77wrap_rot.c:(.text+0x1f): undefined reference to `ATL_drot'
ATL_F77wrap_rot.c:(.text+0x49): undefined reference to `ATL_drot'
ATL_F77wrap_rot.c:(.text+0x78): undefined reference to `ATL_drot'
ATL_F77wrap_rot.c:(.text+0x91): undefined reference to `ATL_drot'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_dspmv.o): In function `atl_f77wrap_dspmv_':
ATL_F77wrap_spmv.c:(.text+0x40): undefined reference to `ATL_dspmv'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_dspr.o): In function `atl_f77wrap_dspr_':
ATL_F77wrap_spr.c:(.text+0x19): undefined reference to `ATL_dspr'
ATL_F77wrap_spr.c:(.text+0x44): undefined reference to `ATL_dspr'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_dsymv.o): In function `atl_f77wrap_dsymv_':
ATL_F77wrap_symv.c:(.text+0x4d): undefined reference to `ATL_dsymv'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_dsyr2.o): In function `atl_f77wrap_dsyr2_':
ATL_F77wrap_syr2.c:(.text+0x41): undefined reference to `ATL_dsyr2'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_dtpmv.o): In function `atl_f77wrap_dtpmv_':
ATL_F77wrap_tpmv.c:(.text+0x18): undefined reference to `ATL_dtpmv'
ATL_F77wrap_tpmv.c:(.text+0x45): undefined reference to `ATL_dtpmv'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_dtpsv.o): In function `atl_f77wrap_dtpsv_':
ATL_F77wrap_tpsv.c:(.text+0x18): undefined reference to `ATL_dtpsv'
ATL_F77wrap_tpsv.c:(.text+0x45): undefined reference to `ATL_dtpsv'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_dtrmv.o): In function `atl_f77wrap_dtrmv_':
ATL_F77wrap_trmv.c:(.text+0x25): undefined reference to `ATL_dtrmv'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_dsymm.o): In function `atl_f77wrap_dsymm_':
ATL_F77wrap_symm.c:(.text+0x54): undefined reference to `ATL_dsymm'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_dsyr2k.o): In function `atl_f77wrap_dsyr2k_':
ATL_F77wrap_syr2k.c:(.text+0x54): undefined reference to `ATL_dsyr2k'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_dznrm2.o): In function `atl_f77wrap_dznrm2_':
ATL_F77wrap_nrm2.c:(.text+0x12): undefined reference to `ATL_dznrm2'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_izamax.o): In function `atl_f77wrap_izamax_':
ATL_F77wrap_amax.c:(.text+0xd): undefined reference to `ATL_izamax'
ATL_F77wrap_amax.c:(.text+0x31): undefined reference to `ATL_izamax'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_zswap.o): In function `atl_f77wrap_zswap_':
ATL_F77wrap_swap.c:(.text+0x11): undefined reference to `ATL_zswap'
ATL_F77wrap_swap.c:(.text+0x32): undefined reference to `ATL_zswap'
ATL_F77wrap_swap.c:(.text+0x61): undefined reference to `ATL_zswap'
ATL_F77wrap_swap.c:(.text+0x70): undefined reference to `ATL_zswap'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_zgemv.o): In function `atl_f77wrap_zgemv_':
ATL_F77wrap_gemv.c:(.text+0x75): undefined reference to `ATL_zgemv'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_zgerc.o): In function `atl_f77wrap_zgerc_':
ATL_F77wrap_gerc.c:(.text+0x35): undefined reference to `ATL_zgerc'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_zgeru.o): In function `atl_f77wrap_zgeru_':
ATL_F77wrap_geru.c:(.text+0x35): undefined reference to `ATL_zgeru'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_zhemv.o): In function `atl_f77wrap_zhemv_':
ATL_F77wrap_hemv.c:(.text+0x41): undefined reference to `ATL_zhemv'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_zher2.o): In function `atl_f77wrap_zher2_':
ATL_F77wrap_her2.c:(.text+0x35): undefined reference to `ATL_zher2'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_zher2k.o): In function `atl_f77wrap_zher2k_':
ATL_F77wrap_her2k.c:(.text+0x43): undefined reference to `ATL_zher2k'
/home/vlado/PROG/lib/atlas/lib/libf77blas.a(ATL_F77wrap_ztrsm.o): In function `atl_f77wrap_ztrsm_':
ATL_F77wrap_trsm.c:(.text+0x25): undefined reference to `ATL_ztrsm'
collect2: ld returned 1 exit status
make[2]: *** [dalton.x] Error 1
make[2]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
make[1]: *** [CMakeFiles/dalton.x.dir/all] Error 2
make[1]: Leaving directory `/home/vlado/PROG/DALTON/DALTON-Source/build_gfortran'
make: *** [all] Error 2
Sorry for bothering, but any idea what is wrong now?
Regards,
Vlado

taylor
Posts: 597
Joined: 15 Oct 2013, 05:37
First name(s): Peter
Middle name(s): Robert
Last name(s): Taylor
Affiliation: Tianjin University
Country: China

Re: make test failed

Post by taylor » 08 Jun 2015, 18:13

It looks like you built your own ATLAS library (since it's in your path)? Is this also built/rebuilt now with g44 etc (or even better a more recent compiler --- I don't use gcc/gfortran myself but the version installed on my laptop appears to be 4.7.2 and I suspect there are several newer versions)? I think you must try to ensure that the entire software stack you're using is pretty much consistent. Mixing and matching from different compiler versions may be a source of difficulty.

Best regards
Pete

taylor
Posts: 597
Joined: 15 Oct 2013, 05:37
First name(s): Peter
Middle name(s): Robert
Last name(s): Taylor
Affiliation: Tianjin University
Country: China

Re: make test failed

Post by taylor » 08 Jun 2015, 18:14

P.S. I probably don't need to add this, but the reason for my question is that clearly you have some issues/incompatibility with the ATLAS library.

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