Compile yambo-3.2.3-rev.11

Having trouble compiling the Yambo source? Using an unusual architecture? Problems with the "configure" script? This is the place to look.

Moderators: Daniele Varsano, andrea.ferretti, andrea marini, Conor Hogan, myrta gruning

Forum rules
If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message

Re: Compile yambo-3.2.3-rev.11

Postby myrta gruning » Wed May 25, 2011 11:28 am

Hallo

maybe you can just try to stop the mpich2 demons (should be mpdallexit) and start them again. Well this if you can do such a thing and if you are not running other jobs under mpich2
this will just tell you if there are problems with mpi demons.

m
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Re: Compile yambo-3.2.3-rev.11

Postby sdwang » Wed Jun 01, 2011 3:30 am

Dear developers:
I try to complie v-3.2.4 with ./configure FC=ifort F77=ifort CC=icc, it is OK in this process, when I >make, it appears:
make[1]: Leaving directory `/vol5/home/jlwang/sdwang/yambo/yambo-3.2.4-r.855/src/xc_functionals'
make: *** [yambo] Error 2

1) the compiler ( intel 9.0)
(2) the architecture (x86_64-redhat-linux/4.1.2-42/,HP clusters)
(3)compiling in parallel
(4) the version of Yambo (yambo-3.2.4-r.855)
Attachment is my config.log.
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Re: Compile yambo-3.2.3-rev.11

Postby claudio » Wed Jun 01, 2011 8:44 am

Dear Shudong Wang

may you configure yambo with the optzions

./configure FC=ifort FC=ifort F77=ifort CC=icc --enable-msgs-comps

and tell us which is the error message you get during compilation.

Remeber to do a

make cleanall

before the new configure

cla
Claudio Attaccalite
Institut Neel, CNRS/UJF ABINEEL group
25 rue des Martyrs BP 166, Bâtiment D
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Re: Compile yambo-3.2.3-rev.11

Postby sdwang » Wed Jun 01, 2011 8:55 am

It is also dump :?。The error as mentioned afore.
# [VER] 3.2.4 r.855
#
# [SYS] linux@x86_64
# [SRC] /vol5/home/jlwang/sdwang/yambo/yambo-3.2.4-r.855
# [BIN] /vol5/home/jlwang/sdwang/yambo/yambo-3.2.4-r.855/bin
# [FFT] FFTW Fast Fourier transform
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [ ] PW (4.0) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [ ] LibXC
# [ ] NETCDF/HDF5/Large Files
# [XX ] Built-in BLAS/LAPACK/LOCAL
#
# [ CPP ] icc -E -ansi
# [ C ] icc -g -O2 -D_C_US -D_FORTRAN_US
# [MPICC] mpicc -g -O2 -D_C_US -D_FORTRAN_US
# [ F90 ] ifort -assume bscc -O3 -ip -tpp7
# [MPIF ] mpif90 -assume bscc -O3 -ip -tpp7
# [ F77 ] ifort -assume bscc -O3 -ip -tpp7
# [Cmain] -nofor_main
# [NoOpt] -assume bscc -O0 -tpp7
#
# [ MAKE ] make
# [EDITOR] vim

error:
>>>[Making xc_functionals]<<<
make[1]: Entering directory `/vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/src/xc_functionals'
mod_xc_costants.F xc_rpa_kp.F xcspol.F(22): error: incorrectly formed universal character name
!! zeta(npts)=$(\rho\uparrow-\rho\downarrow)/(\rho\uparrow+\rho\downarrow)$=degree of polarization
^

xcspol.F(22): error: incorrectly formed universal character name
!! zeta(npts)=$(\rho\uparrow-\rho\downarrow)/(\rho\uparrow+\rho\downarrow)$=degree of polarization
^

xcspol.F(28): error: incorrectly formed universal character name
!! if(nspden=1 .and. order==-2): also compute dvxc(:,2)=dvxc($\uparrow$)/d$\rho(\downarrow)$
^

xcspol.F(29): error: incorrectly formed universal character name
!! if(nspden=2): dvxc(:,1)=dvxc($\uparrow$)/d$\rho(\uparrow)$,
^

xcspol.F(29): error: incorrectly formed universal character name
!! if(nspden=2): dvxc(:,1)=dvxc($\uparrow$)/d$\rho(\uparrow)$,
^

xcspol.F(30): error: incorrectly formed universal character name
!! dvxc(:,2)=dvxc($\uparrow$)/d$\rho(\downarrow)$, dvxc(:,3)=dvxc($\downarrow$)/d$\rho(\downarrow)$
^

xcspol.F(33): error: incorrectly formed universal character name
!! vxc(npts,nspden)=xc potent. (d($\rho$*exc)/d($\rho\uparrow$)) and d/d($\rho\downarrow$) (ha)
^

xcspol.F(59): error: incorrectly formed universal character name
!! zeta = $(\rho\uparrow-\rho\downarrow)/(\rho\uparrow+\rho\downarrow)$
^

xcspol.F(59): error: incorrectly formed universal character name
!! zeta = $(\rho\uparrow-\rho\downarrow)/(\rho\uparrow+\rho\downarrow)$
^

make[1]: *** [xcspol.o] Error 2
make[1]: Leaving directory `/vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/src/xc_functionals'
make: *** [yambo] Error 2
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Re: Compile yambo-3.2.3-rev.11

Postby myrta gruning » Sat Jun 11, 2011 9:54 pm

Dear Shudong

sdwang wrote:It is also dump :?。The error as mentioned afore.


the flag suggested by Claudio "--enable-msgs-comps" was to enable the messaging during compilation error so to understand what goes wrong.

Apparently it is the precompiler. It is a bit weird because I am also using ifort+icc and I do not have this problem. It may be the version of the compiler, I am using v11.1 [anyway from your config it seems you are mixing two different versions of the compiler, v10.1 for icc and v9 for ifort...]

You can try a different precompiler. gcc should be available.
After a make clean, reconfigure with
./configure FC=ifort FC=ifort F77=ifort CC=icc CPP=gcc --enable-msgs-comps
and see if it compiles.

Good luck ;)
m
Dr Myrta Grüning
Atomistic Simulation Centre
Queen's University Belfast - Northern Ireland

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Re: Compile yambo-3.2.3-rev.11

Postby sdwang » Sun Jun 12, 2011 4:31 am

Dear developers:
It does not work.The error is the same.
I have found in my ./bashrc, it appears:
source /opt/intel/fce/10.1.018/bin/ifortvars.sh
source /opt/intel/mkl/10.2.2.025/tools/environment/mklvarsem64t.sh

The mkl is 10.2 but intel/fce is 10.1.Does this relate to the error?
S D Wang
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Re: Compile yambo-3.2.3-rev.11

Postby claudio » Sun Jun 12, 2011 8:08 am

Dear Shudong

do a make clean_all
configure yambo with the --enable-msgs-comps
then compile it as

make yambo &> output_compilation

and send us the "output_compilation" file

Cla
Claudio Attaccalite
Institut Neel, CNRS/UJF ABINEEL group
25 rue des Martyrs BP 166, Bâtiment D
38042 Grenoble cedex 9 France
web site: http://www.attaccalite.com
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Re: Compile yambo-3.2.3-rev.11

Postby sdwang » Sun Jun 12, 2011 8:29 am

[quote="claudio"]Dear Shudong

do a make clean_all
configure yambo with the --enable-msgs-comps
then compile it as

make yambo &> output_compilation

and send us the "output_compilation" file

Cla[/quote
In attachment is the output_compilation.
Thanks!
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Re: Compile yambo-3.2.3-rev.11

Postby claudio » Mon Jun 13, 2011 10:52 pm

Dear Shudong

it seems that you icc doesn't like some comment in a fortran file, but I'm not able to reproduce
this error with my icc.

So you can try different things:
1) edit the file src/xc_functionals/xcspol.F and remove the first 68 lines, the comments, and recompile all
2) upgrade your icc to the last version
3) try a different preprocessor for example cpp, doing ./configure FC=ifort F77=ifort CPP=/usr/bin/cpp

let me know
Claudio
Claudio Attaccalite
Institut Neel, CNRS/UJF ABINEEL group
25 rue des Martyrs BP 166, Bâtiment D
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web site: http://www.attaccalite.com
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Re: Compile yambo-3.2.3-rev.11

Postby sdwang » Sat Jun 18, 2011 9:23 am

I used the first method, and it has problem when linking yambo :
>>>[Linking yambo]<<<
make[1]: Entering directory `/vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver'
if test ! -f __lock_D_FFTW && test "yes" = "no" ; then find . \( -name '*.o' -o -name '*.mod' -o -name '__*' \) | xargs rm -f ; touch __lock_D_FFTW; fi
if test "yes" = "yes"; then "/vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855"/sbin/objects_debug.sh __lock_D_FFTW; fi
(eval /opt/intel/cce/10.1.018/bin/icc -E -ansi -D_MPI -D_FFTW -D_linux yambo_driver.F > yambo_driver.f90) > /dev/null
(mpif90 -c -assume bscc -O3 -ip -xW -nofor_main -I /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/include -I/vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/include yambo_driver.f90) > /dev/null
yambo_driver.F if test -f /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver/yambo.h; then /opt/intel/cce/10.1.018/bin/icc -E -ansi -D_MPI -D_FFTW -D_linux /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver/yambo.h > /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver/yambo_cpp.h; fi
if test -f /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver/ypp.h; then /opt/intel/cce/10.1.018/bin/icc -E -ansi -D_MPI -D_FFTW -D_linux /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver/ypp.h > /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver/ypp_cpp.h; fi
( eval /opt/intel/cce/10.1.018/bin/icc -g -O2 -D_C_US -D_FORTRAN_US -c /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver/getopt.c > /dev/null)
if test "yes" = ""; then /opt/intel/cce/10.1.018/bin/icc -g -O2 -D_C_US -D_FORTRAN_US -D_MPI -D_FFTW -D_linux -D_yambo -c /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver/driver.c; fi
if test ! "yes" = ""; then mpicc -g -O2 -D_C_US -D_FORTRAN_US -D_MPI -D_FFTW -D_linux -D_yambo -c /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver/driver.c; fi
rm -f /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver/yambo_cpp.h /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver/ypp_cpp.h

(eval mpif90 -assume bscc -O3 -ip -xW -nofor_main -I /vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/include -o yambo driver.o getopt.o yambo_driver.o -L/vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/lib -lbse -lqp -lpol_function -ltddft -linterface -lsetup -lqp_ctl -lbz_ops -lcoulomb -lwf_and_fft -lio -lcommon -lcommunicate -lparser -lxc_functionals -lmodules -lexternal_c -llapack -lblas -lslatec -lfftw3 -lm ) > /dev/null
IPO link: can not find "("
ifort: error: problem during multi-file optimization compilation (code 1)
make[1]: *** [yambo] Error 1
make[1]: Leaving directory `/vol5/home/jlwang/workspace/sdwang/yambo/yambo-3.2.4-r.855/driver'
make: *** [yambo] Error 2

The config is: ./configure FC=/opt/intel/fce/10.1.018/bin/ifort F77=/opt/intel/fce/10.1.018/bin/ifort --enable-msgs-comps --with-iotk=/vol5/home/jlwang/workspace/sdwang/espresso-4.3/iotk/ --with-p2y=4.0 CC=/opt/intel/cce/10.1.018/bin/icc cpp=/vol5/gcc/gcc-4.5.1/bin/cpp
S. D. Wang
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E-mail: sdwang@imu.edu.cn
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