[petsc-users] Reading a complex vector from HDF5

x 1D vector is saves as a 2D real valued vector of shape dim,2. I've done the same with my data and yet I get the above error. Is there any special precaution I should take when making the HDF5 file ? Thank You, Sajid Ali Applied Physics Northwestern University

[petsc-users] petsc4py for numpy array <-> MATDENSE binary

script. Does petsc4py support converting a 3d numpy array (complex valued) to MATDENSE (MPI) binary format directly ? I saw some discussion on this topic back in 2012 on the mailing list but it's not clear to me what happened after that. Thank You, Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] Question about TSSetRHSJacobian for linear time dependent problem

The form is u_t = A(t)u. On Sun, Jan 27, 2019 at 4:24 PM Smith, Barry F. wrote: > > > > On Jan 25, 2019, at 4:51 PM, Sajid Ali via petsc-users < > petsc-users@mcs.anl.gov> wrote: > > > > Hi, > > > > If I have a linear time dependent equat

[petsc-users] Question about TSSetRHSJacobian for linear time dependent problem

iteration but that unnecessarily doubles the memory consumption, is there a better way? Thank You, Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] VecCopy fails after VecDuplicate

with VecSetValues, I missed out on adding VecAssembleBegin/End to compensate. Thanks for pointing out that the error was with u and not u_abs. On Thu, Jan 17, 2019 at 1:29 PM Sajid Ali wrote: > As requested : > > [sajid@xrm free_space]$ ./ex_modify > Solving a linear TS problem on 1 process

Re: [petsc-users] VecCopy fails after VecDuplicate

As requested : [sajid@xrm free_space]$ ./ex_modify Solving a linear TS problem on 1 processor m : 256, slices : 1000.00, lambda : 1.239800e-10 [0]PETSC ERROR: - Error Message -- [0]PETSC ERROR: Object is in wrong

[petsc-users] VecCopy fails after VecDuplicate

statements doesn't help either : ierr = VecAssemblyBegin(u_abs);CHKERRQ(ierr); ierr = VecAssemblyEnd(u_abs);CHKERRQ(ierr); If needed, the entire file is at : https://github.com/s-sajid-ali/xwp_petsc/blob/master/1d/free_space/ex_modify.c Thank You, Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] Question about correctly catching fp_trap

> Anyway the FPE occurs in MatSolve_SeqAIJ_NaturalOrdering which usually indicates a zero on the diagonal of the matrix. Is that possible? It looks like this is indeed the case here. Thanks for the hint. @Satish Balay : I tried building with the patch and don't see any difference. Do you want

Re: [petsc-users] Question about correctly catching fp_trap

Trying it slightly differently, I do see it's a SIGFPE, arithmetic exception but all it shows is that it's an error in TSSolve but no further than that. [sajid@xrm free_space]$ gdb ex_modify GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-100.el7 Copyright (C) 2013 Free Software Foundation, Inc.

Re: [petsc-users] Question about correctly catching fp_trap

Going by the advice given here : https://stackoverflow.com/a/2792735 I tried running the program, hoping to catch the FP exception and I got the error I had before (which turned out to be due to an FP exception as per previous petsc thread): Missing separate debuginfos, use: debuginfo-install

Re: [petsc-users] Question about correctly catching fp_trap

I asked in the spack-slack channel and was told to include the explicitly link the gfortran associated with the gcc version I build petsc with. Following that advice, I'm using gcc@7.3.0, linking gcc@7.3.0/lib64 in FFLAGS and setting -g option to CFLAGS in my makefile. Yet, somehow the executable

Re: [petsc-users] Question about correctly catching fp_trap

Should gdb : https://spack.readthedocs.io/en/latest/package_list.html#gdb be listed as an explicit dependency ? Also, why is the error message asking me to re-install my system blas/lapack ? I installed petsc with intel-mkl as blas/lapack provider and the linking failed for superlu-dist. Is that

Re: [petsc-users] Question about correctly catching fp_trap

Spack changes the configuration if debug variant is enabled as per this line : '--with-debugging=%s' % ('1' if '+debug' in spec else '0'), I'm not sure what needs to be done to change this. In the meantime, I added -g to CFLAGS in the makefile and now I have this : https://pastebin.com/wxf05BH0

[petsc-users] Question about correctly catching fp_trap

? Thank You, Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] Set diagonals other than main diagonal

Got it. Thank you! On Thu, Jan 3, 2019 at 11:46 AM Matthew Knepley wrote: > On Thu, Jan 3, 2019 at 12:24 PM Sajid Ali via petsc-users < > petsc-users@mcs.anl.gov> wrote: > >> Hi, >> >> Is there any simple way of setting minor diagonals. The main diagona

[petsc-users] Set diagonals other than main diagonal

Hi, Is there any simple way of setting minor diagonals. The main diagonal can be set by MatDiagonalSet but there's no equivalent way of doing it for for minor diagonals. Does the preferred way to do this involve using MatSetValues or there a simpler way? Thank You, Sajid Ali Applied Physics

Re: [petsc-users] Some questions about TS/examples/tutorials/ex13

> No, A(t) has five diagonals as indicated by the calls to MatSetValues() with five entries per row; they correspond to the usual 5 pt stencil in 2d. This might not be the right place to ask this, but I'm new to PDE's and I expected to find something like the matrix to be used as the one derived

[petsc-users] Some questions about TS/examples/tutorials/ex13

petsc stores 2d vectors? Thank You, Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] Question about PetscViewerHDF5SetTimestep usage

I tried running the same with petsc@develop and it worked. But if the fix was committed on Dec5, then it should in theory work with petsc@3.10.3 . I'm not sure why it doesn't work either.

Re: [petsc-users] Question about PetscViewerHDF5SetTimestep usage

The example is the same as above. Link : https://pastebin.com/cAeZsUgA Here's what happens when I try to compile and run using petsc@3.10.3: https://pastebin.com/EGVSxJu5 Thank You, Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] Question about PetscViewerHDF5SetTimestep usage

Dec 14, 2018 at 4:04 PM Sajid Ali < > sajidsyed2...@u.northwestern.edu> wrote: > >> Hi Matthew, >> >> Thanks for the info. Could you give a specific commit that I should >> rebuild PETSc with ? I’m currently building with >> commit=83593104eb216a023c00a

Re: [petsc-users] Question about PetscViewerHDF5SetTimestep usage

bug in HDF5 attribute > creation. > > Thanks, > > Matt > > On Fri, Dec 14, 2018 at 1:16 PM Sajid Ali via petsc-users < > petsc-users@mcs.anl.gov> wrote: > >> Hi, >> >> I have a question about PetscViewerHDF5SetTimestep usage. >> >&g

[petsc-users] Question about PetscViewerHDF5SetTimestep usage

something wrong ? Thank You, Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] X-Viewer for complex numbers

Specifically in the context of drawing a vector using the X-viewer ( PetscDraw ). On Wed, Dec 12, 2018 at 9:33 AM Sajid Ali wrote: > Hi , > > Does petsc automatically convert complex valued vectors to absolute value > vectors before passing it to a viewer ? Is there a way to vi

[petsc-users] X-Viewer for complex numbers

Hi , Does petsc automatically convert complex valued vectors to absolute value vectors before passing it to a viewer ? Is there a way to view the phase of a vector ? Thank You, Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] PETSc binary write format

For future reference, attached is a snippet of code in C to convert ascii numbers (integers and doubles) to petsc readable binary vectors. -- Sajid Ali Applied Physics Northwestern University ascii_to_bin.c Description: Binary data

Re: [petsc-users] PETSc binary write format

I'm attaching the file vector.dat and the file petsc saves (vec_old.dat) with this email. Thank You, Sajid Ali Applied Physics Northwestern University vector.dat Description: Binary data vec_old.dat Description: Binary data

Re: [petsc-users] PETSc binary write format

. On Wed, Dec 5, 2018 at 12:57 PM Sajid Ali wrote: > It's just a cleaner re-write of the petsc output that I can understand > (which I intend to modify from python in the future). I tried removing the > new line characters but that didn't work either. > > Looking at the first line of

Re: [petsc-users] PETSc binary write format

s well. Thank You, Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] PETSc binary write format

Exactly. When I run ex10 and inspect it with cat, I get garbage since the data is in binary : [sajid@xrm temp]$ cat vector.dat {N?�▒@@ @"@$@&@(@*@,@.@0@1@2@3[sajid@xrm temp]$ But doing a binary dump shows the data : [sajid@xrm temp]$ xxd -b vector.dat 000: 00010010 0011

Re: [petsc-users] PETSc binary write format

I have created a file as per the specification as shown below [sajid@xrm temp]$ cat vector.dat 00010010001101001110 00010100 0011

Re: [petsc-users] PETSc binary write format

For future reference, the numbers do look like they're stored as per IEEE 754 64-bit convention. I don't know what the special characters in the xxd output are but the size of the file is consistent with 2*int_32+num_elements*dobule_64. Thank you ! Sajid Ali Applied Physics Northwestern

Re: [petsc-users] PETSc binary write format

, Barry F. wrote: > >You saved a Vec to the file, not a Mat. > > > > > On Dec 3, 2018, at 1:38 PM, Sajid Ali via petsc-users < > petsc-users@mcs.anl.gov> wrote: > > > > Hi, > > > > I ran ex10 from /vec/examples/tutorials and saved the ma

[petsc-users] PETSc binary write format

s 1211214, but the value of MAT_FILE_CLASSID according to the header file petscmat.h is 1211216 ( petsc@3.10.2.1 built without complex support). What causes this discrepancy ? Also, what are the special characters at the end of every line ? Am i not reading the binary file correctly ? Thank You, Sajid Al

Re: [petsc-users] Error in vec/vec/examples/tutorials/ex19.c

rote: > > > > On Nov 30, 2018, at 1:30 PM, Sajid Ali via petsc-users < > petsc-users@mcs.anl.gov> wrote: > > > > Hi, > > > > I tried running ex19.c and I get the following error (I added a small > snippet to print the local size on rank0 as well) : > >

Re: [petsc-users] Load dense matrices from hdf5

That is > r0 i0 r1 i1 where r0 is the first matrix entry's real part and i0 > is the first matrix imaginary part. > > Barry > > > > On Nov 30, 2018, at 5:04 PM, Sajid Ali > wrote: > > > > If the matrix is filled with complex numbers is eac

Re: [petsc-users] Load dense matrices from hdf5

If the matrix is filled with complex numbers is each complex number stored as a sequences of doubles ? Or is it better to split the matrix into real/imaginary and store each part separately?

Re: [petsc-users] Load dense matrices from hdf5

u are getting your h(t) values from). > > Barry > > > > On Nov 30, 2018, at 4:27 PM, Sajid Ali via petsc-users < > petsc-users@mcs.anl.gov> wrote: > > > > Hi, > > > > I'm trying to solve the Helmholtz equation in 1D for x-rays which > roughly l

[petsc-users] Load dense matrices from hdf5

Hi, I'm trying to solve the Helmholtz equation in 1D for x-rays which roughly like : u_dot = a*u_xx + h(t)*u I've already implemented <https://github.com/s-sajid-ali/xwp_petsc/blob/master/1d/free_space/ex_modify.c> the case where h(t) is always zero (free-space) in PETSc as per the la

[petsc-users] Error in vec/vec/examples/tutorials/ex19.c

that PETSC_DECIDE is inconsistent between two calls in the same file ? Thank You, Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] Some clarifications about TS ex3.c

if it's less than tolerance ? I commented out the norm calculation (lines 404-415) the time is stuck at 0 ( as per the output of -ts_monitor). But if I comment out the above lines (417-422) as well, everything works fine. What explains this behaviour ? Thank You! Sajid Ali Applied Physics Northwestern University

[petsc-users] Some clarifications about TS ex3.c

ed before calling TSSetIJacobian. Does this mean that the TSSetIJacobian takes care of the shift ? 3) What is happening on line 198 ? Thank You, Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] Question about DMDAGetElements

Bingo! So, DMDAGetElements gives the indices of the mesh, right ? Thank you !

Re: [petsc-users] Question about DMDAGetElements

So, DMDA is used for sparse matrices arising from FD/FE and MatCreateMPIAIJ can be used for dense matrices (though it is strongly discouraged). My confusion stemmed from DMDAGetElements giving the element indices for the 1D mesh/vector of size N(when the DMDACreate1d is used). But these indices

Re: [petsc-users] Question about DMDAGetElements

at each rank (for the submatrix stored locally) add up to the size of the total matrix). Is my understanding correct? Thanks for the help! -- Sajid Ali Applied Physics Northwestern University

Re: [petsc-users] Question about DMDAGetElements

. Is this correct? 3) How would the indices obtained from DMDAGetElements correspond to the indices for a vector created using DMCreateGlobalVector ? Thank You, Sajid Ali Applied Physics Northwestern University

[petsc-users] Question about DMDAGetElements

Hi, I'm trying to understand this example from a tutorial. DM is used as an alternative to setting up the matrix and vector separately (as was done in the previous example

Re: [Pw_forum] "Lanczos.x with k-point algorithm"

= 0.005d0, p_nbnd_occ = 50 p_nbnd_virt = 50 / For turbo_spectrum.x _input prefix='BN', outdir='./', itermax=500 itermax0=100 end=3.50d0 extrapolation='osc' increment=0.0001d0 start=0.0d0 td= 'davidson', eign_file = 'BN.eigen', / Cheers SAJID ALI Cell#+61449764974 Ph.D

Re: [Pw_forum] "Lanczos.x with k-point algorithm"

NaN NaN SAJID ALI Cell#+61449764974 Ph.D. Scholar School of Mathematical and Physical Sciences University of Technology, Sydney Australia From: Sajid Ali Sent: 18 January 2016 05:05 To: Iurii Timrov Cc: PWSCF Forum

Re: [Pw_forum] "Lanczos.x with k-point algorithm"

Dear, Iurii Timrov i am Sorry, It was a typo, i meant QE-5.3.0. SAJID ALI Cell#+61449764974 Ph.D. Scholar School of Mathematical and Physical Sciences University of Technology, Sydney Australia From: Iurii Timrov <itim...@sissa.it> Sent: 17 J

Re: [Pw_forum] "Lanczos.x with k-point algorithm"

Dear, Iurii Timrov I have tried using QE-5.5.0 for both SCF and TDDFPT But i recieived similar kind of error in lanczos.x output i.e. "mpirun noticed that process rank 1 with PID 1046 on node ermdc06 exited on signal 11 (Segmentation fault)". Cant find a way out of it....?

Re: [Pw_forum] "Lanczos.x with k-point algorithm"

, ipol = 1, / [ _post epsil = 0.0004d0 ] /" SAJID ALI Cell#+61449764974 Ph.D. Scholar School of Mathematical and Physical Sciences University of Technology, Sydney Australia From: Iurii Timrov <itim...@sissa.it> Sent: 15 January 2016 17:10 To: PWSCF Fo

[Pw_forum] "Lanczos.x with k-point algorithm"

anczos iteration: 2 Pol:1 -- mpirun noticed that process rank 20 with PID 62359 on node c3node01 exited on signal 11 (Segmentation fault). ------ SAJID ALI Cell#+61449764974 Ph.D. Scholar School of Ma

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*DUBAI MARINA * *1 B/R + HALL IN MARINA TERRACE WITH MARINA VIEW 1080 sqft RENT = 80K* STUDIO IN ZUMURUD TOWER AREA = 400 sqft RENT = 40K *2 B/R + HALL IN GULF NATIONAL 1350 sqf * *RENT = 80K* *2 B/R + HALL + LAUNDRY IN IRIS BLUE 1570 sqft RENT = 125K* *GREENS* *2 B/R FULLY FURNISHED

[dubairentals:13234] properties for rent

*DUBAI MARINA * *1 B/R + HALL IN MARINA TERRACE WITH MARINA VIEW** 1080 sqft RENT = 80K* *1 B/R + HALL IN MARINA DIAMOND-6** 850 sqft RENT = 50K* *1 B/R + HALL IN PANORAMIC BUILDING ** 730sqft RENT = 60K* *1 B/R + HALL IN AZURE BUILDING ** 850 sqft RENT = 60K* *1 B/R + HALL IN MARINA CROWN

[dubairentals:13242] properties for rent

*DUBAI MARINA * *1 B/R + HALL IN MARINA TERRACE WITH MARINA VIEW** 1080 sqft RENT = 80K* *1 B/R + HALL IN MARINA DIAMOND-6** 850 sqft RENT = 50K* *1 B/R + HALL IN MARINA CROWN ** 850 sqft RENT = 55K* *2 B/R + HALL IN GULF NATIONAL** 1350 sqft RENT = 80K* *2 B/R + HALL + LAUNDRY IN IRIS

[dubairentals:13248] properties for rent

*DUBAI MARINA * *1 B/R + HALL IN MARINA TERRACE WITH MARINA VIEW 1080 sqft RENT = 80K* *1 B/R + HALL IN MARINA DIAMOND-6 850 sqft RENT = 50K* *1 B/R + HALL IN MARINA CROWN 850 sqft RENT = 55K* *2 B/R + HALL IN GULF NATIONAL 1350 sqft RENT = 80K* *2 B/R + HALL + LAUNDRY IN IRIS BLUE 1570

[dubairentals:13249] propeerties for rent

*DUBAI MARINA * *1 B/R + HALL IN MARINA TERRACE WITH MARINA VIEW 1080 sqft RENT = 80K* *1 B/R + HALL IN MARINA DIAMOND-6 850 sqft RENT = 50K* *1 B/R + HALL IN MARINA CROWN 850 sqft RENT = 55K* *2 B/R + HALL IN GULF NATIONAL 1350 sqft RENT = 80K* *2 B/R + HALL + LAUNDRY IN IRIS BLUE 1570

[Openjdk] [Bug 581994] Re: Eclipse craches(noreason) after upgrading to Ubuntu 10.04

I am facing the same problem... It occurs when we try to use auto complete option. #A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x015becee, pid=20786, tid=2993884016 # # JRE version: 6.0_18-b18 # Java VM: OpenJDK Client VM (16.0-b13 mixed mode,

[Bug 581994] Re: Eclipse craches(noreason) after upgrading to Ubuntu 10.04

I am facing the same problem... It occurs when we try to use auto complete option. #A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x015becee, pid=20786, tid=2993884016 # # JRE version: 6.0_18-b18 # Java VM: OpenJDK Client VM (16.0-b13 mixed mode,

Investors Club Dubai - Alert Properties For Rent

DUBAI MARINA 1 B/R + HALL IN MARINA TERRACE 1080 sq.ft RENT =80K 1 B/R + HALL IN MARINA DIAMOND -6 850 sqft RENT = 50K 1 B/R + HALL IN PANORAMIC 850 sqft RENT = 60K 1 B/R + HALL IN AZRE 850 sqft RENT =60K 1 B/R + HALL IN MARINA CROWN 850 sqft RENT = 60K 2 B/R + HALL IN GULF NATIONAL 1350

Investors Club Dubai - Alert properties for rent

INTERNATIONAL CITY NICE 1 B/R + HALL IN SPAIN cluster WITH BALCONY SQ.FT = 750 RENT =33K NICE 1 B/R + HALL IN GREECE cluster WITH BALCONY SQ.FT = 750 RENT = 30K DUBAI MARINA FULLY FRUNISHED 1 B/R + HALL IN MARINA TERRACE WITH BALCONY SQFT 1080 RENT = 85K NICE 1 B/R + HALL IN MARINA CROWN

Investors Club Dubai - Alert properties for rent

INTERNATIONAL CITY NICE 1 B/R + HALL IN SPAIN cluster WITH BALCONY SQ.FT = 750 RENT =33K NICE 1 B/R + HALL IN GREECE cluster WITH BALCONY SQ.FT = 750 RENT = 30K DUBAI MARINA FULLY FRUNISHED 1 B/R + HALL IN MARINA TERRACE WITH BALCONY SQFT 1080 RENT = 85K NICE 1 B/R + HALL IN MARINA CROWN

Investors Club Dubai - Alert properties for rent

INTERNATIONAL CITY NICE 1 B/R + HALL IN SPAIN cluster WITH BALCONY SQ.FT = 750 RENT =33K NICE 1 B/R + HALL IN GREECE cluster WITH BALCONY SQ.FT = 750 RENT = 30K DUBAI MARINA FULLY FRUNISHED 1 B/R + HALL IN MARINA TERRACE WITH BALCONY SQFT 1080 RENT = 85K NICE 1 B/R + HALL IN MARINA CROWN WITH

Investors Club Dubai - Alert properties for rent

INTERNATIONAL CITY NICE 1 B/R + HALL IN SPAIN cluster WITH BALCONY 750 sq.ft RENT =33K NICE 1 B/R + HALL IN GREECE cluster WITH BALCONY SQ.FT = 750 RENT = 30K DUBAI MARINA FULLY FRUNISHED 1 B/R + HALL IN MARINA TERRACE WITH BALCONY 1080 sq.ft RENT = 85K NICE 1 B/R + HALL IN MARINA CROWN WITH

Investors Club Dubai - Alert PROPERTIES FOR RENT

INTERNATIONAL CITY NICE 1 B/R + HALL IN SPAIN WITH BALCONY SQ.FT = 750 RENT =33K NICE 1 B/R + HALL IN GREECE WITH BALCONY SQ.FT = 750 RENT = 30K DUBAI MARINA FULLY FRUNISHED 1 B/R + HALL IN MARINA TERRACE WITH BALCONY SQFT 1080 RENT = 85K NICE 1 B/R + HALL IN MARINA CROWN WITH BALCONY SQFT =

Investors Club Dubai - Alert PROPETIES FOR RENT

INTERNATIONAL CITY NICE 1 B/R + HALL IN SPAIN CLUSTER WITH BALCONY SQ.FT = 750 RENT =33K NICE 1 B/R + HALL IN GREECE CLUSTER WITH BALCONY SQ.FT = 750 RENT = 30K DUBAI MARINA FULLY FRUNISHED 1 B/R + HALL IN MARINA TERRACE WITH BALCONY SQFT 1080 RENT = 85K NICE 1 B/R + HALL IN MARINA CROWN WITH

Investors Club Dubai - Alert properties for rent

INTERNATIONAL CITY NICE 1 B/R + HALL IN SPAIN cluster WITH BALCONY SQ.FT = 750 RENT =33K NICE 1 B/R + HALL IN GREECE cluster WITH BALCONY SQ.FT = 750 RENT = 30K DUBAI MARINA FULLY FRUNISHED 1 B/R + HALL IN MARINA TERRACE WITH BALCONY SQFT 1080 RENT = 85K NICE 1 B/R + HALL IN MARINA CROWN WITH

[jboss-user] [Beginner's Corner] - Presentation of Services in JBoss SOA?

Sajid Ali [http://community.jboss.org/people/sajidali143] created the discussion Presentation of Services in JBoss SOA? To view the discussion, visit: http://community.jboss.org/message/543341#543341 -- Hi every one, first of all i

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