Linking problem with ypp on an IBM server

[vormar]

Dear all,

I faced a linking problem while trying to compile yambo-3.2.1-r.506 on Magerit-CeSViMa. This supercomputer consists of IBM PowerPC servers (BladeCenter JS20 and JS21). My problem is that I could compile and link yambo and p2y, however there was an error while linking ypp:

(eval mpif90 -q64 -O3 -qnoescape -qnostrict -qarch=ppc970 -qtune=ppc970 -I/gpfs/projects/ehu35/maurizia/D_marton/yambo-3.2.1/include -o ypp driver.o getopt.o mod_YPP.o ypp_i.o ypp_init.o ypp_init_load.o k_grids.o excitons_driver.o electrons_driver.o plot_check_and_launch.o plot_gnuplot.o plot_xcrysden.o excitons_sort_and_report.o -L/gpfs/projects/ehu35/maurizia/D_marton/yambo-3.2.1/lib -lbse -linterface -lsetup -lqp_ctl -lbz_ops -lwf_and_fft -lio -lcommon -lcommunicate -lparser -lxc_functionals -lmodules -lexternal_c /gpfs/apps/LAPACK/3.0/64/liblapack.a /gpfs/apps/BLAS/1.0.0/64/lib/libblas.a -lnetcdf -llocal -lm ) > /dev/null
/gpfs/projects/ehu35/maurizia/D_marton/yambo-3.2.1/lib/libbse.a(K_output_file.o):(.text+0x270): undefined reference to `o_eels'
/gpfs/projects/ehu35/maurizia/D_marton/yambo-3.2.1/lib/libbse.a(K_output_file.o):(.text+0xce0): undefined reference to `o_eels'
/gpfs/projects/ehu35/maurizia/D_marton/yambo-3.2.1/lib/libbse.a(K_output_file.o):(.text+0x1600): undefined reference to `o_eels'
/gpfs/projects/ehu35/maurizia/D_marton/yambo-3.2.1/lib/libbse.a(K_output_file.o):(.text+0x1f20): undefined reference to `o_eels'
make[1]: *** [ypp] Error 1
make[1]: Leaving directory `/gpfs/projects/ehu35/maurizia/D_marton/yambo-3.2.1_test/ypp'
make: *** [ypp] Error 2

I searched through the forum and the source as well, hoping that there is a trivial problem, and I also tried to modify the configure options (see the original version below), but I could only worsen things. Anyway, it seems that yambo and p2y binaries work well, at least I got reasonable results.

Here are the options I pass to configure:
PF90=xlf90_r FC=xlf90_r F77=xlf_r CC=xlc_r CPP="cpp -E -P" --with-blas=/gpfs/apps/BLAS/1.0.0/64/lib/libblas.a --with-lapack=/gpfs/apps/LAPACK/3.0/64/liblapack.a --with-p2y=4.0 --with-iotk=/gpfs/projects/ehu35/espresso-4.0.5/iotk --with-netcdf-include=/gpfs/apps/NETCDF/3.6.0/64/include --with-netcdf-lib=/gpfs/apps/NETCDF/3.6.0/64/lib --with-fftw=/gpfs/apps/FFTW/3.2/64/lib --enable-msgs-comps=no

Lapack, blas, fftw libraries and espresso were built by the support, and the version of the IBM fortran/c compiler is 12.1/10.1.

Any help will be appreciated. I could send further details on the compilation if needed.

Yours,
Marton

#-------------------------------------------------#
# M\'arton V\"or\"os #
# PhD student #
# Department of Atomic Physics, #
# Budapest University of Technology and Economics #
# Budafoki út 8., H-1111, Budapest, Hungary #
# http://www.fat.bme.hu/MartonVoros #
#-------------------------------------------------#

[myrta gruning]

Hello Marton,

Maybe xlf is stricter than other compilers. I do not know since I am not using it. (you may look at http://www.yambo-code.org/doc/compiling.php , there is something on xlf). So maybe other people know better... The following may be a quick fix.

It is true that o_eels, called in one of the library (libbse) that "you" are linking is not referenced. Other compilers seem to be fine with that.

You may try to add -lpol_function when linking (e.g. you can add it in the ypp/Makefile under "llibs=", I am not sure of the order, try just before or after -lbse, save and close the file, and do "make" just in that directory, e.g. ypp)

Of course linking pol_function may lead to more undefined references . In that case all the libs that are needed are in the folder lib (*.a) in your yambo dir, you can see what is in there using "ar -t somelib.a", e.g

Code: Select all

myrta@aiken:~/Sources/yambo_gpl/lib$ ar -t libpol_function.a
O_driver.o
O_eels.o
Dipole_driver.o
Dipole_kb_pp_comp.o
Dipole_kb_sum.o
Dipole_kb_Ylm.o
Dipole_transverse.o
X_drude.o
X_pre_setup.o
X_simple_GreenF.o
X_eh_setup.o
X_em1.o
X_os.o
X_s.o
X_delta_part.o
X_bare_RIM_GreenF.o
O_select_q_and_G.o

I hope this help.

Let us know.
m

PS Please edit your signature in the user control panel (the profile tab), in that way it will be included automatically to all your post! Thanks.

[vormar]

Dear Myrta,

Your quick fix worked: putting -lpol_function after -lbse in ypp/Makefile, row "llibs=" solved the problem, now I have a working ypp executable. Thank you for your fast reply!

(signature edited)

Yours,
Marton

[vormar]

Dear Myrta,

It seems that I spoke too soon... I was so happy to get it linked. I was mistaken that "ypp -H" would actually tell if ypp works or not. Unfortunately, now I have the following problem if I try to generate an input with ypp:

Code: Select all

 /gpfs/projects/ehu35/maurizia/D_marton/yambo-3.2.1_test/bin/ypp -N -s s
"mod_com.f", line 286: 1525-101 The file name provided in the INQUIRE statement contains a null character.  The program will recover by using a file name of ..
"mod_com.f", line 286: 1525-100 The file name provided in the INQUIRE statement has zero length or contains all blanks.  The program will recover by ignoring the INQUIRE statement.


[ERROR] STOP signal received while in :
[ERROR][NetCDF] Is a directory

Do you have any idea what happens?

Furthermore, I think I found a small bug. After I had a compilation failure with mod_logo.f (note the suffix ".f", in the makefile I have f90suffix = .f), it wasn't removed after make clean_all. Therefore if I recompiled the code with new (and good) compiler options, the same compiler error appeared. I don't really know if this is a real problem, but the file mod_parser_m.f also remained after the compilation failure.

Yours,
Marton

[andrea marini]

Do you have any idea what happens?

The problem is solved reducing the optimization option. -O3 seems to be too aggressive for some parts of the code. I have taken note of changing the optimization to -O2 for modules, for example. In this case, indeed, it is mod_com.F and mod_IO.F that up messed up by the xlf optimization.

So, as temporary work-around, you can either pass the correct options to the configure or change the config/setup (after running the configure) according to

f90flags = -q64 -O2 -qnoescape -qnostrict -qarch=ppc970 -qtune=ppc970
pf90flags = -q64 -O2 -qnoescape -qnostrict -qarch=ppc970 -qtune=ppc970
f77flags = -q64 -O2 -qnoescape -qnostrict -qarch=ppc970 -qtune=ppc970