[Smeagol-discuss] segmentation fault
Ivan Rungger
runggeri at tcd.ie
Thu Mar 26 14:28:52 GMT 2009
Hello,
I also think that you are running out of memory as Salvador says. One
reason for that is that you use a large number of energy points. Try using
NEnergReal 0
NEnergImCircle 16
NEnergImLine 16
NPoles 16
VInitial 0.0 eV
VFinal 0.0 eV
NIVPoints 0
You don't need more imaginary energy points for T=300K. A note: just
make sure that NEnergImCircle+NEnergImLine+2* NPoles is a multiple of
the number or processors you are running on (although from your
debugging message it seems you are running in serial). And another
thing: I would only do the zero bias calculation, because applying a
bias to a nanotube without contacting it to some metal surface might not
be physically meaningful (although I have to say that I did not check in
detail your setup, therefore maybe it might also be OK to apply a bias).
Cheers,
Ivan
Barraza-lopez, Salvador wrote:
>
> Forgot to mention... you can use the output from your debug run to see
> what's going on... What's happening on line 570 at negf.F?
>
> Have you tried if SZ will run?
>
>
>
> Best regards,
>
> -Salvador.
>
>
> ----- Original Message -----
> From: "Serhan Yamacli" <syamacli at gmail.com>
> To: "Salvador Barraza-lopez" <sbl3 at mail.gatech.edu>,
> smeagol-discuss at lists.tchpc.tcd.ie
> Sent: Sunday, March 22, 2009 4:44:43 AM GMT -05:00 US/Canada Eastern
> Subject: Re: [Smeagol-discuss] segmentation fault
>
> Hi,
>
> I compiled with these options. And then googled for the error and
> found that it's a memory error as you said. I increased the stack size
> by the command ulimit -s unlimited. The program now does not give
> segmentation error but instead gives the "insufficient virtual memory"
> error. I've also attached the screenshot of the system resources at
> their maximum when running Smeagol. Now the problem is that Smeagol
> uses 165MB of RAM at maximum (just before it gives error) but I have
> 2GB of RAM with 4GB of swap. It can not gather the remaining RAM which
> is more then 1GB and gives the following error:
>
> ----------------------------------------------------------------------------------------------------------------
> * Maximum dynamic memory allocated = 174 MB
> gensvd: Leads decimation
> gensvd: Dim of H1 and S1 : 468
> gensvd: Rank of H1: 49
> gensvd: Rank of (H1,S1): 154
> gensvd: Decimated states: 265
> gensvd: Decimation from the left
> gensvd: Leads decimation
> gensvd: Dim of H1 and S1 : 468
> gensvd: Rank of H1: 49
> gensvd: Rank of (H1,S1): 154
> gensvd: Decimated states: 265
> gensvd: Decimation from the left
> forrtl: severe (41): insufficient virtual memory
> Image PC Routine Line
> Source
> smeagol 0831F29D Unknown Unknown Unknown
> smeagol 0831E815 Unknown Unknown Unknown
> smeagol 082DB838 Unknown Unknown Unknown
> smeagol 0829BB43 Unknown Unknown Unknown
> smeagol 082C4380 Unknown Unknown Unknown
> smeagol 081CEDAC negf_ 570 negf.F
> smeagol 082679E3 emtg_ 280 emtg.F
> smeagol 0826DE62 emtrans_ 208 emtrans.F
> smeagol 08194A98 MAIN__ 1698 siesta.F
> smeagol 0804B4D1 Unknown Unknown Unknown
> libc.so.6 40B5A685 Unknown Unknown Unknown
> smeagol 0804B3E1 Unknown Unknown Unknown
>
> ---------------------------------------------------------------------------------------------------------------------
>
> Thanks again.
> Cheers
> Serhan
>
>
> 2009/3/21 Barraza-lopez, Salvador <sbl3 at mail.gatech.edu
> <mailto:sbl3 at mail.gatech.edu>>
>
> When you compile it, use -O0 -g -traceback. I guess you are using
> gcc?
>
>
>
> My gut feeling is you don't have sufficient memory to run it...
> The important number here is
>
> initatomlists: Number of atoms, orbitals, and projectors: 60
> 540 960
> the number of orbitals. You say it decreased when you changed
> your basis size. The 540 is 1s, 3p and 5d per 60 atoms (9*60=540).
> It went down from 13*60= 780 that you had before... In any case,
> try running it in debug mode and use top at the same time.
>
>
>
> as an additional test, try SZ for your basis, that'll give you 4
> orbitals per atom, matrices of size 240x240. If it crashes, try
> compiling in debug mode.
>
>
>
> Also, investigate in google what segmentation fault means. I do
> believe is a memory related issue.
>
>
>
> Best,
>
> -Salva.
>
>
>
>
> ----- Original Message -----
> From: "Serhan Yamacli" <syamacli at gmail.com
> <mailto:syamacli at gmail.com>>
> To: "Salvador Barraza-lopez" <sbl3 at mail.gatech.edu
> <mailto:sbl3 at mail.gatech.edu>>
> Sent: Saturday, March 21, 2009 1:48:02 PM GMT -05:00 US/Canada Eastern
> Subject: Re: [Smeagol-discuss] segmentation fault
>
> I'm using Smeagol at a single machine in serial mode. The CPU is
> 2.26GHz and memory available is 2GB. How can I run it in debug mode?
>
> Cheers
> Serhan
>
> 2009/3/21 Barraza-lopez, Salvador <sbl3 at mail.gatech.edu
> <mailto:sbl3 at mail.gatech.edu>>
>
> can you run it in debug mode? can you share the output? how
> much memory do you have available per processor?
>
>
>
> Best,
>
> -Salvador.
>
>
>
>
> ----- Original Message -----
> From: "Serhan Yamacli" <syamacli at gmail.com
> <mailto:syamacli at gmail.com>>
> To: "Salvador Barraza-lopez" <sbl3 at mail.gatech.edu
> <mailto:sbl3 at mail.gatech.edu>>,
> smeagol-discuss at lists.tchpc.tcd.ie
> <mailto:smeagol-discuss at lists.tchpc.tcd.ie>
> Sent: Saturday, March 21, 2009 11:59:38 AM GMT -05:00
> US/Canada Eastern
> Subject: Re: [Smeagol-discuss] segmentation fault
>
> Hi Salvador,
>
> I looked at the system resources as you said. Smeagol
> executable takes 26% of memory at maximum, then it gives the
> segmentation fault error.
>
> Best regards,
> Serhan
>
> 2009/3/21 Barraza-lopez, Salvador <sbl3 at mail.gatech.edu
> <mailto:sbl3 at mail.gatech.edu>>
>
>
>
> Hi Serhan,
>
> Can you check the dynamic memory in your run? I believe
> the problem is related to this but I may be wrong.
>
>
>
> you can log in to the running node, type top and get an
> idea of the total memory as the program goes.
>
>
>
> Best regards,
>
> -Salvador.
>
>
> ----- Original Message -----
> From: "Serhan Yamacli" <syamacli at gmail.com
> <mailto:syamacli at gmail.com>>
> To: "Salvador Barraza-lopez" <sbl3 at mail.gatech.edu
> <mailto:sbl3 at mail.gatech.edu>>
> Sent: Saturday, March 21, 2009 11:19:03 AM GMT -05:00
> US/Canada Eastern
> Subject: Re: [Smeagol-discuss] segmentation fault
>
> Hi Salvador,
>
> Thanks for the answer but, Smeagol again gives the error
> when changed basis to SZP:
>
> -----------------------------------------------------------------------------------------
> initatomlists: Number of atoms, orbitals, and
> projectors: 60 540 960
>
> siesta: System type = chain
>
> * Maximum dynamic memory allocated = 1 MB
>
> siesta: ===============================
> SMEAGOL Bias step = 0, V = 0.000 Ry
> Begin CG move = 0
> ===============================
>
> InitMesh: MESH = 180 x 180 x 108 = 3499200
> InitMesh: Mesh cutoff (required, used) = 200.000
> 212.441 Ry
>
> * Maximum dynamic memory allocated = 279 MB
> Segmentation fault
>
> -------------------------------------------------------------------------------------
>
> I again attached the modidied input fdf.
>
> Cheers,
> Serhan
> 2009/3/21 Barraza-lopez, Salvador <sbl3 at mail.gatech.edu
> <mailto:sbl3 at mail.gatech.edu>>
>
> Hi Serhan, how about reducing the basis size to SZP?
>
>
>
> Best regards,
>
> -Salvador.
>
>
> ----- Original Message -----
> From: "Serhan Yamacli" <syamacli at gmail.com
> <mailto:syamacli at gmail.com>>
> To: smeagol-discuss at lists.tchpc.tcd.ie
> <mailto:smeagol-discuss at lists.tchpc.tcd.ie>
> Sent: Saturday, March 21, 2009 10:34:06 AM GMT -05:00
> US/Canada Eastern
> Subject: [Smeagol-discuss] segmentation fault
>
> Hi,
>
> I'm trying to simulate a (3,3) intrinsic carbon
> nanotube. I performed the leads calculation. But when
> I try to simulate the transport, Smeagol says:
>
> --------------------------------------------------------------------------------------------------------------
> initatomlists: Number of atoms, orbitals, and
> projectors: 60 780 960
>
> siesta: System type = chain
>
> * Maximum dynamic memory allocated = 1 MB
>
> siesta: ===============================
> SMEAGOL Bias step = 0, V = 0.000 Ry
> Begin CG move = 0
> ===============================
>
> InitMesh: MESH = 240 x 240 x 150 = 8640000
> InitMesh: Mesh cutoff (required, used) = 400.000
> 409.800 Ry
>
> * Maximum dynamic memory allocated = 727 MB
> Segmentation fault
>
> -------------------------------------------------------------------------------------------------------
>
> My fdf file is atteched. How can I solve this problem?
> I'm using Mandriva 2008 with ifort.
>
> Cheers
> Serhan
>
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--
=================================================
Ivan Rungger,
School of Physics and CRANN,
Trinity College Dublin,
Dublin 2, IRELAND
Phone: +353-1-8968454
Email: runggeri at tcd.ie
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