[Wien] NMR calculations failed

Robert Laskowski rolask at ihpc.a-star.edu.sg
Mon Jan 27 08:58:35 CET 2014 

Hi,

I would advice to update the SRC_NMR. Such things like that should be gone in
the current version.

regards

Robert



On 27 January 2014 PM 3:50:53 Gavin Abo wrote:
> It may or may not be related to the problem, but it looks like after it
> prints the line
>
> k-point    1 ... done,  timings (fopv, cs,ci, tot):   4935.04    359.16
> 111.30   5407.25
>
> in SRC_nmr/make_current.frc of Wien2k 13.1, it has the following two
> lines (201 and 203)
>
>                deallocate(weigh,evec,gvec,ene)
>
> totmemcon=totmemcon-size(evec)*rcmemfac-size(gvec)*imemfac
>
> These lines run just fine (at least on my system) with gfortran and
> ifort.  However, it seems strange to me that evec and gvec are being
> used after they have just been deallocated.
>
> On 1/24/2014 12:02 AM, Bing Zhou wrote:
> > Dear all,
> > I can run "x_nmr_lapw" successfully, however, after run "x_nmr_lapw
> > -noinit -emin -0.45 -emax 0.0033", it crashed and I encountered the
> > following error, could you please help me fix it? Thank you in advance!
> > Bing
> >
> > EXECUTING:     /global/software/wien2k-13/bin/nmr -case probertite-opt-DOS
> > -mode current    -green    -emin -0.45 -emax 0.0033   -nocore -scratch
> > /scratch/>
> >        -noco
> >
> > k-point    1 ... done,  timings (fopv, cs,ci, tot):   4935.04    359.16
> > 111.30   5407.25 *** glibc detected ***
> > /global/software/wien2k-13/bin/nmr: double free or corruption (!prev):
> > 0x0000000000cd4e90 *** ======= Backtrace: =========
> > /lib64/libc.so.6[0x3df14760e6]
> > /lib64/libc.so.6[0x3df1478c13]
> > /global/software/wien2k-13/bin/nmr[0x4cab2c]
> > /global/software/wien2k-13/bin/nmr[0x473870]
> > /global/software/wien2k-13/bin/nmr[0x46970b]
> > /global/software/wien2k-13/bin/nmr[0x4454b0]
> > /global/software/wien2k-13/bin/nmr[0x410c7f]
> > /global/software/wien2k-13/bin/nmr[0x403b2c]
> > /lib64/libc.so.6(__libc_start_main+0xfd)[0x3df141ecdd]
> > /global/software/wien2k-13/bin/nmr[0x403a29]
> > ======= Memory map: ========
> > 00400000-005a3000 r-xp 00000000 00:14 72801963
> > /global/software/wien2k-13/bin/nmr 007a3000-007ba000 rw-p 001a3000 00:14
> > 72801963                           /global/software/wien2k-13/bin/nmr
> > 007ba000-007f1000 rw-p 00000000 00:00 0
> > 00c9a000-06f33000 rw-p 00000000 00:00 0
> > [heap] 3df0c00000-3df0c20000 r-xp 00000000 08:03 1057202
> >       /lib64/ld-2.12.so 3df0e1f000-3df0e20000 r--p 0001f000 08:03 1057202
> >                        /lib64/ld-2.12.so 3df0e20000-3df0e21000 rw-p
> > 00020000 08:03 1057202                        /lib64/ld-2.12.so
> > 3df0e21000-3df0e22000 rw-p 00000000 00:00 0
> > 3df1000000-3df1083000 r-xp 00000000 08:03 1057234
> > /lib64/libm-2.12.so 3df1083000-3df1282000 ---p 00083000 08:03 1057234
> >                    /lib64/libm-2.12.so 3df1282000-3df1283000 r--p
> > 00082000 08:03 1057234                        /lib64/libm-2.12.so
> > 3df1283000-3df1284000 rw-p 00083000 08:03 1057234
> > /lib64/libm-2.12.so 3df1400000-3df158a000 r-xp 00000000 08:03 1057203
> >                    /lib64/libc-2.12.so 3df158a000-3df1789000 ---p
> > 0018a000 08:03 1057203                        /lib64/libc-2.12.so
> > 3df1789000-3df178d000 r--p 00189000 08:03 1057203
> > /lib64/libc-2.12.so 3df178d000-3df178e000 rw-p 0018d000 08:03 1057203
> >                    /lib64/libc-2.12.so 3df178e000-3df1793000 rw-p
> > 00000000 00:00 0
> > 3df1800000-3df1802000 r-xp 00000000 08:03 1057209
> > /lib64/libdl-2.12.so 3df1802000-3df1a02000 ---p 00002000 08:03 1057209
> >                     /lib64/libdl-2.12.so 3df1a02000-3df1a03000 r--p
> > 00002000 08:03 1057209                        /lib64/libdl-2.12.so
> > 3df1a03000-3df1a04000 rw-p 00003000 08:03 1057209
> > /lib64/libdl-2.12.so 3df1c00000-3df1c17000 r-xp 00000000 08:03 1057204
> >                     /lib64/libpthread-2.12.so 3df1c17000-3df1e17000 ---p
> > 00017000 08:03 1057204                        /lib64/libpthread-2.12.so
> > 3df1e17000-3df1e18000 r--p 00017000 08:03 1057204
> > /lib64/libpthread-2.12.so 3df1e18000-3df1e19000 rw-p 00018000 08:03
> > 1057204                        /lib64/libpthread-2.12.so
> > 3df1e19000-3df1e1d000 rw-p 00000000 00:00 0
> > 3df2c00000-3df2c16000 r-xp 00000000 08:03 1057222
> > /lib64/libgcc_s-4.4.7-20120601.so.1 3df2c16000-3df2e15000 ---p 00016000
> > 08:03 1057222                        /lib64/libgcc_s-4.4.7-20120601.so.1
> > 3df2e15000-3df2e16000 rw-p 00015000 08:03 1057222
> > /lib64/libgcc_s-4.4.7-20120601.so.1 2ae753c21000-2ae753c23000 rw-p
> > 00000000 00:00 0
> > 2ae753c23000-2ae753db8000 r-xp 00000000 00:14 51680799
> > /global/software/fftw-3.3.3-intel12-mpi/lib/libfftw3.so.3.3.2
> > 2ae753db8000-2ae753fb8000 ---p 00195000 00:14 51680799
> > /global/software/fftw-3.3.3-intel12-mpi/lib/libfftw3.so.3.3.2
> > 2ae753fb8000-2ae753fc4000 rw-p 00195000 00:14 51680799
> > /global/software/fftw-3.3.3-intel12-mpi/lib/libfftw3.so.3.3.2
> > 2ae753fc4000-2ae754596000 r-xp 00000000 00:14 53747059
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_intel_ lp64.so
> > 2ae754596000-2ae754796000 ---p 005d2000 00:14 53747059
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_intel_ lp64.so
> > 2ae754796000-2ae7547a5000 rw-p 005d2000 00:14 53747059
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_intel_ lp64.so
> > 2ae7547a5000-2ae7547aa000 rw-p 00000000 00:00 0
> > 2ae7547aa000-2ae7554ce000 r-xp 00000000 00:14 53747063
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_intel_ thread.so
> > 2ae7554ce000-2ae7556ce000 ---p 00d24000 00:14 53747063
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_intel_ thread.so
> > 2ae7556ce000-2ae755826000 rw-p 00d24000 00:14 53747063
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_intel_ thread.so
> > 2ae755826000-2ae75582a000 rw-p 00000000 00:00 0
> > 2ae75582a000-2ae756672000 r-xp 00000000 00:14 53747048
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_core.s o
> > 2ae756672000-2ae756871000 ---p 00e48000 00:14 53747048
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_core.s o
> > 2ae756871000-2ae756885000 rw-p 00e47000 00:14 53747048
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_core.s o
> > 2ae756885000-2ae756895000 rw-p 00000000 00:00 0
> > 2ae7568ae000-2ae7568af000 rw-p 00000000 00:00 0
> > 2ae7568af000-2ae75697b000 r-xp 00000000 00:14 53491637
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/compiler/lib/intel
> > 64/libiomp5 .so
> > 2ae75697b000-2ae756b7a000 ---p 000cc000 00:14 53491637
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/compiler/lib/intel
> > 64/libiomp5 .so
> > 2ae756b7a000-2ae756b84000 rw-p 000cb000 00:14 53491637
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/compiler/lib/intel
> > 64/libiomp5 .so
> > 2ae756b84000-2ae772390000 rw-p 00000000 00:00 0
> > 2ae772390000-2ae773f3c000 r-xp 00000000 00:14 53747067
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_mc3.so 2ae773f3c000-2ae77413b000 ---p 01bac000 00:14 53747067
> >
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_mc3.so 2ae77413b000-2ae774191000 rw-p 01bab000 00:14 53747067
> >
> > /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/li
> > bmkl_mc3.so 2ae774191000-2ae789cf9000 rw-p 00000000 00:00 0
> > 2ae78b685000-2ae83e300000 rw-p 00000000 00:00 0
> > 7fffe5d12000-7fffe5d9a000 rw-p 00000000 00:00 0
> > [stack] 7fffe5dff000-7fffe5e00000 r-xp 00000000 00:00 0
> >        [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
> >              [vsyscall] Abort
> >
> > stop error
>
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--
==================================================
Dr. Robert Laskowski

Senior Scientist, Materials Science & Engineering Department
Institute of High Performance Computing, A*STAR
1 Fusionopolis Way, #16-16, Connexis, Singapore 138632
Tel(Off): +65. 64191493     Fax: +65. 64632536
=================================================

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