Thanks for your kind words. The library mkl_gf_lp64 was caught by the configuration script after sourcing the mkl libraries.
Yasser -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Davide Ceresoli Sent: Monday, January 30, 2017 3:04 PM To: PWSCF Forum <[email protected]> Subject: Re: [Pw_forum] qe-gipaw 6.0 Segmentation fault Dear Yasser, I'm glad it works! notwithstanding that you link the gfortran MKL (mkl_gf_lp64), zdotc still need a workaround, interesting! It seems to me that you are already using FFT from MKL (-D__DFTI). Best, Davide On 01/29/2017 04:21 PM, Yasser Fowad AlWahedi wrote: > Dear Paolo and Davide, > > Thank you so much for your kind help. I have tested solutions 1,2 and 4 > since the 3 was not applicable. Two solutions of the suggested ones worked. > For the sake of record; I have put below the details of my trials and the > outcomes I got as to help any one who might be facing this problem in the > future. > > > My GNU compilers versions is: GNU Fortran (Ubuntu > 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609 > > the successful make.inc file is attached. > > > Solution 1 (failed): I modified the greenfunction.f90 in the src under gipaw > to: > > eprec (ibnd) = 1.35d0 * sum(conjg(evq(1:npw,ibnd))*work(1:npw)) !zdotc > (npw, evq (1, ibnd), 1, work, 1) > > recompiled gipaw.x and tested again, here I got the following error > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > > Backtrace for this error: > #0 0x7F6A0A0A6E08 > #1 0x7F6A0A0A5F90 > #0 0x7F2817102E08 > #2 0x7F6A095BB4AF > #1 0x7F2817101F90 > #2 0x7F28166174AF > #3 0x7F6A0CF5B2CD > #3 0x7F2819FB72CD > #0 0x7FB0AF7DBE08 > #0 0x7F334BB99E08 > #0 0x7FCA597BCE08 > #1 0x7FB0AF7DAF90 > #1 0x7F334BB98F90 > #1 0x7FCA597BBF90 > #2 0x7FCA58CD14AF > #2 0x7FB0AECF04AF > #3 0x#2 0x7F334B0AE4AF > #3 0x7FCA5C6712CD > 7FB0B26902CD > #3 0x7F334EA4E2CD > #0 0x7FAB00A1DE08 > #1 0x7FAB00A1CF90 > #0 0x7F9E42A5DE08 > #2 0x7FAAFFF324AF > #3 0x7FAB038D22CD > #1 0x7F9E42A5CF90 > #2 0x7F9E41F724AF > #3 0x7F9E459122CD > #0 0x7F6E3302AE08 > #1 0x7F6E33029F90 > #2 0x7F6E3253F4AF > #3 0x7F6E35EDF2CD > #0 0x7F7F133A2E08 > #0 0x7F1935284E08 > #1 0x7F7F133A1F90 > #1 0x7F1935283F90 > #2 0x7F7F128B74AF > #2 0x7F19347994AF > #3 0x7F7F162572CD > #3 0x7F19381392CD > #4 0x412E66 in cgsolve_all_ at cgsolve_all.f90:148 (discriminator 2) > #4 0x412E66 in cgsolve_all_ at cgsolve_all.f90:148 (discriminator 2) > #5 0x411E6A in greenfunction_ at greenfunction.f90:257 > #5 0x411E6A in greenfunction_ at greenfunction.f90:257 > #4 0x412E66 in cgsolve_all_ at cgsolve_all.f90:148 (discriminator 2) > #4 0x412E66 in cgsolve_all_ at cgsolve_all.f90:148 (discriminator 2) > #5 0x411E6A in greenfunction_ at greenfunction.f90:257 > #6 0x43070A in paramagnetic_correction_aug_ at nmr_routines.f90:375 > #4 0x412E66 in cgsolve_all_ at cgsolve_all.f90:148 (discriminator 2) > #6 0x43070A in paramagnetic_correction_aug_ at nmr_routines.f90:375 > #5 0x411E6A in greenfunction_ at greenfunction.f90:257 > #4 0x412E66 in cgsolve_all_ at cgsolve_all.f90:148 (discriminator 2) > #5 0x411E6A in greenfunction_ at greenfunction.f90:257 > #4 0x412E66 in cgsolve_all_ at cgsolve_all.f90:148 (discriminator 2) > #4 0x412E66 in cgsolve_all_ at cgsolve_all.f90:148 (discriminator 2) > #5 0x411E6A in greenfunction_ at greenfunction.f90:257 > #5 0x411E6A in greenfunction_ at greenfunction.f90:257 > #4 0x412E66 in cgsolve_all_ at cgsolve_all.f90:148 (discriminator 2) > #7 0x41E9C9 in suscept_crystal_inner_qzero at suscept_crystal.f90:469 > #5 0x411E6A in greenfunction_ at greenfunction.f90:257 > #8 0x4053F2 in MAIN__ at gipaw_main.f90:155 > #5 0x411E6A in greenfunction_ at greenfunction.f90:257 > #4 0x412E66 in cgsolve_all_ at cgsolve_all.f90:148 (discriminator 2) > #6 0x43070A in paramagnetic_correction_aug_ at nmr_routines.f90:375 > #7 0x41E9C9 in suscept_crystal_inner_qzero at suscept_crystal.f90:469 > #6 0x43070A in paramagnetic_correction_aug_ at nmr_routines.f90:375 > #5 0x411E6A in greenfunction_ at greenfunction.f90:257 > #6 0x43070A in paramagnetic_correction_aug_ at nmr_routines.f90:375 > #8 0x4053F2 in MAIN__ at gipaw_main.f90:155 > #6 0x43070A in paramagnetic_correction_aug_ at nmr_routines.f90:375 > #6 0x43070A in paramagnetic_correction_aug_ at nmr_routines.f90:375 > #6 0x43070A in paramagnetic_correction_aug_ at nmr_routines.f90:375 > #6 0x43070A in paramagnetic_correction_aug_ at nmr_routines.f90:375 > #7 0x41E9C9 in suscept_crystal_inner_qzero at suscept_crystal.f90:469 > #6 0x43070A in paramagnetic_correction_aug_ at nmr_routines.f90:375 > #7 0x41E9C9 in suscept_crystal_inner_qzero at suscept_crystal.f90:469 > #7 0x41E9C9 in suscept_crystal_inner_qzero at suscept_crystal.f90:469 > #8 0x4053F2 in MAIN__ at gipaw_main.f90:155 > #8 0x4053F2 in MAIN__ at gipaw_main.f90:155 > #8 0x4053F2 in MAIN__ at gipaw_main.f90:155 > #7 0x41E9C9 in suscept_crystal_inner_qzero at suscept_crystal.f90:469 > #7 0x41E9C9 in suscept_crystal_inner_qzero at suscept_crystal.f90:469 > #7 0x41E9C9 in suscept_crystal_inner_qzero at suscept_crystal.f90:469 > #7 #8 0x4053F2 in MAIN__ at gipaw_main.f90:155 > #8 0x4053F2 in MAIN__ at gipaw_main.f90:155 > 0x41E9C9 in #8 0x4053F2 in MAIN__ at gipaw_main.f90:155 > suscept_crystal_inner_qzero at suscept_crystal.f90:469 > #7 0x41E9C9 in suscept_crystal_inner_qzero at suscept_crystal.f90:469 > #8 0x#8 0x4053F2 in MAIN__ at gipaw_main.f90:155 > 4053F2 in MAIN__ at gipaw_main.f90:155 > > Solution 2: I used the existing Netlib math libs compiled everything as is > using GNU compilers without any change to the greenfunction.f90. > > This worked fine and I managed to get the magres file. > > Of course I prefer to use intel mkl since in benchmark cases I ran it was 3 > to 5 times faster than Netlib. > > Solution 4: Add the line -Dzdotc=zdotc_wrapper to > DFLAGS in make.inc then compile with GNU, intel mkl and fftw3 > > This solution worked perfectly without any problems and produced the same > result of solution 2. Thanks again for your help. > > One small question; to use the FFT library of intel mkl what libraries should > i add to the make.inc file? > > Yasser > > ________________________________________ > From: [email protected] [[email protected]] on > behalf of Paolo Giannozzi [[email protected]] > Sent: Sunday, January 29, 2017 1:19 PM > To: PWSCF Forum > Subject: Re: [Pw_forum] qe-gipaw 6.0 Segmentation fault > > 3) re-link with -lmkl_gf_lp64 instead of -lmkl_intel_lp64, or > 4) re-compile with preprocessing option -Dzdotc=zdotc_wrapper added to > DFLAGS > > Paolo > > On Sun, Jan 29, 2017 at 10:07 AM, Davide Ceresoli > <[email protected]> wrote: >> Dear Yasser, >> can you tell us the compiler version, and send the generated >> make.inc? The crash is on the very first call to 'zdotc' which >> returns a complex (128 bit) and I suspect an incompatibility between >> GNU compilers and Intel MKL. >> >> While I'm checking this, could you try two things? >> 1) modify greenfunction.f90:209 from: >> eprec (ibnd) = 1.35d0 * zdotc (npw, evq (1, ibnd), 1, work, 1) >> to: >> eprec (ibnd) = 1.35d0 * sum( conjg(evq(1:npw,inbd)) * work(1:npw) ) >> >> 2) recompile without mkl? configure with --with-netlib or with any >> other blas/lapack implementation. >> >> Best, >> Davide >> >> >> >> >> On 01/27/2017 03:23 PM, Yasser Fowad AlWahedi wrote: >>> Dear all, >>> >>> I have compiled QE 6.0 with GNU compilers, intel mkl for all >>> libraries except fft which i used fftw3 for it. I used MPICH for the MPI >>> libs. >>> >>> I also compiled successfully gipaw version 6.0 using the same >>> libraries. I started running the quartz example. SCF went successfully >>> without any problems. >>> >>> GIPAW failed and gave the following error: >>> >>> /Program received signal SIGSEGV: Segmentation fault - invalid memory >>> reference. >>> >>> Backtrace for this error: >>> #0 0x7F050C81AE08 >>> #1 0x7F050C819F90 >>> #2 0x7F050BD2F4AF >>> #3 0x7F050F6CF2CD >>> #4 0x411A17 in greenfunction_ at greenfunction.f90:209 >>> #5 0x43069A in paramagnetic_correction_aug_ at nmr_routines.f90:375 >>> #6 0x41E959 in suscept_crystal_inner_qzero at >>> suscept_crystal.f90:469 >>> #7 0x4053F2 in MAIN__ at gipaw_main.f90:155 Segmentation fault >>> (core dumped)/ >>> >>> I ran using 1 core and 10 cores, both gave similar errors. >>> >>> I checked other posts and it seems a similar problem existed before >>> in version 5.4. I assumed it was fixed in version 6.0. Can you >>> please advise on what can i do to address this problem? >>> >>> Yasser Al Wahedi >>> Assistant Professor >>> Petroleum Institute >>> >> _______________________________________________ >> Pw_forum mailing list >> [email protected] >> http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone > +39-0432-558216, fax +39-0432-558222 > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > -- +--------------------------------------------------------------+ Davide Ceresoli CNR Institute of Molecular Science and Technology (CNR-ISTM) c/o University of Milan, via Golgi 19, 20133 Milan, Italy Email: [email protected] Phone: +39-02-50314276, +39-347-1001570 (mobile) Skype: dceresoli Website: http://sites.google.com/site/dceresoli/ +--------------------------------------------------------------+ _______________________________________________ Pw_forum mailing list [email protected] http://pwscf.org/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list [email protected] http://pwscf.org/mailman/listinfo/pw_forum
