[Pw_forum] qe-gipaw 6.0 Segmentation fault

Yasser Fowad AlWahedi yaalwahedi at pi.ac.ae
Sun Jan 29 16:21:44 CET 2017

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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: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] on behalf of Paolo Giannozzi [p.giannozzi at gmail.com]
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
<davide.ceresoli at cnr.it> 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
> Pw_forum at pwscf.org
> 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
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