Akbar, this weird... it could be that, for whatever reason, the system is nor being able to find a library it shouldn't even look for, since you have specified static linking in LDFLAGS. Try adding -pthread before -L/home/akbar/Packages/scalapack-1.8.0, and to LDFLAGS as well just to make sure.
Marcos On Fri, Jul 30, 2010 at 8:47 AM, akbar jahangiri <[email protected]>wrote: > Dear Marcos > > I tried to compile SIESTA package but I faced some difficulties like : > > First the following error which system ( I think ) is not able to find the > library "lpthread_nonshared" > ====================================================================== > > g.o pxf.o libfdf.a libxmlparser.a libmpi_f90.a\ > `FoX/FoX-config --libs --wcml` > -L/home/akbar/Packages/scalapack-1.8.0 -lscalapack > -L/home/akbar/Packages/BLACS/LIB -lblacsF77init -lblacs -L/usr/lib > -lpthread_nonshared > > ld: cannot find -lpthread > make: *** [siesta] Error 1 > ====================================================================== > > But when I search for it in my system I have it as you mention before. > > ===================================================================== > [ak...@mac1 Obj]$ locate libpthread > /lib/libpthread-2.12.so > /lib/libpthread.so.0 > /lib/i686/nosegneg/libpthread-2.12.so > /lib/i686/nosegneg/libpthread.so.0 > /usr/lib/libpthread.so > /usr/lib/libpthread_nonshared.a > ===================================================================== > > what can be the problem ? > > my arch make file is attached too. > > Thank you very much > best regards > Akbar > > > > > > 2010/7/25 Marcos Veríssimo Alves <[email protected]> > > Akbar, >> >> Your system is not being able to find libpthread.a. Usually this is in >> /usr/lib or /usr/lib64, depending on the version of the compiler (32 or 64 >> bits) you are using. Also, if in the compilation options you have -static >> and libpthread.a is not present (but only libpthread.so) then you should use >> libpthread_nonshared.a, which should appear as lpthread_nonshared in the >> list of libraries. >> >> Marcos >> >> >> On Sat, Jul 24, 2010 at 5:08 PM, akbar jahangiri <[email protected]>wrote: >> >>> Dear Marcos >>> >>> Thank you for your guidance. >>> >>> While compiling Siesta-3.0_rc2 I have still problem, I think related to >>> libraries (BLACS). >>> But I have compiled the libraries as you have mentioned in this mail. and >>> I was able to compile them. >>> When I am going to compile SIESTA I get the following error which I think >>> I should not get! (according to my arch.make file ) >>> >>> ========================================================= >>> o get_target_stress.o fire_optim.o zm_fire_optim.o cell_fire_optim.o >>> m_fire_para.o m_fire_mixing.o write_raw_efs.o m_iodm.o m_sparse.o >>> kpoint_pdos.o nag.o pxf.o libfdf.a libxmlparser.a libmpi_f90.a\ >>> `FoX/FoX-config --libs --wcml` >>> -L/home/akbar/Packages/scalapack-1.8.0 -lscalapack >>> -L/home/akbar/Packages/BLACS/LIB -lblacsF77init -lblacs -lblacsCinit >>> ld: cannot find -lpthread >>> make: *** [siesta] Error 1 >>> ============================================================ >>> >>> I am sending the arck.make file too. >>> I should mention in the directory of "BLACS" I did not have the >>> following "libs" (which I have comment them in arch.make file ) >>> >>> >>>-lmkl_lapack -lmkl_em64t -lguide -lpthread_nonshared -lmkl_core << >>> >>> but still siesta is asking for them !!!! >>> >>> could you please let me know what is the problem? >>> >>> Best regards >>> Akbar Jahangiri >>> >>> 2010/7/13 Marcos Veríssimo Alves <[email protected]> >>> >>> Hi all, >>>> >>>> Given that many people are actually having problems compiling whatever >>>> version of Siesta after 2.x, I have decided to send a small, ultra-concise, >>>> step-by-step guide to compile siesta as I have done in my desktop and my >>>> laptop. I suppose it will be the case of many people here, so I forward an >>>> email I sent to a colleague some time ago for the compilation of siesta >>>> 3.0-rc1. I have just tested the executable with the nanotube 5-0 test on a >>>> dual core desktop and it runs fine. So, I expect thos instructions to work >>>> for most multicore computers. >>>> >>>> Steps for compiling Siesta 3.0-rc2 >>>> >>>> 0 - Very very very very very important: *ifort 10.1* *(11, at least >>>> until some time ago, didn't work. It's buggy and it will only waste your >>>> time - and the time of the people of the rest of the list)* and >>>> mkl 10.0.1.014. Again, without this, you'll probably be wasting your time, >>>> and everyone else in the list's as well. Don't forget to set the >>>> environment >>>> variables with the appropriate scripts for ifort and mkl. Also, search >>>> netlib.org for the Blacs and Scalapack. >>>> >>>> 1 - I am using mpich2-1.2.1. If you want to use a newer version, feel >>>> free to do so, but please download mpich2. It's faster to compile, and it's >>>> known to work. >>>> >>>> 2 - Type tar -zxvf for the mpich tarball and, for configuring: >>>> ./configure F77=ifort FFLAGS=-O2 F90=ifort F90FLAGS=-O2 --enable-f90 >>>> >>>> 3 - Type make install. For installing in the default directories, you >>>> will need root access. If you don't have root access, ask the sysadmin or >>>> your closest Linux guru to install ifort 10, the mkl and mpich with the >>>> instructions given in steps 0-3. If you install in "unconventional >>>> directories" then don't forget to inclued them in your PATH environment >>>> variable, preferably before anything else that was already set. >>>> >>>> 4 - With mpich compiled, it's time to compile BLACS. There's no need to >>>> be root for that - just use the one I am sending here. Adapt the Bmake.inc >>>> inside the root directory to reflect the installation directories you need: >>>> mpif90, mpi include files and all that jazz, and type make mpi . >>>> >>>> 5 - Compile scalapack. I am using scalapack 1.7.5. Adapt SLmake.inc as >>>> needed and type make. >>>> >>>> 6 - Use the arch.make included in this email to compile siesta after >>>> having creating the compilation directory with >>>> $SIESTA_HOME/Src/objsetup.sh. >>>> Adapt arch.make to reflect the directories where all the libraries are >>>> found. and type make. >>>> >>>> 7 - Start the mpd and run siesta in parallel (you might end up not being >>>> able to hold some tears, hopefully out of happiness :D ) >>>> >>>> Hope this helps. It is also possible to use the Blacs and Scalapack >>>> included with the mkl, but for this you'll have to search the list archives >>>> after November 2009... >>>> >>>> Cheers, >>>> >>>> Marcos >>>> >>> >>> >> >
