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
make.inc
Description: make.inc
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