[Smeagol-discuss] stay for a long time when running the transport calculations!

[Barraza-lopez, Salvador]

Hi Mingsu, 

The "Leads decimation" messages will occur for each lead, for each spin component, and for each k-point in the extended molecule calculation. 
Your output indicates the size of the matrices involved for the extended molecule: 2006x2006 double complex (16 bits per entry). 

The leads might have sizes relatively smaller than the extended molecule, say 500x500 or so? 
In any event, I would suggest to log in to the running nodes and execute "top" on them. That way you will have a look at the memory usage. It may be that allocation of memory is taking long, or else that your job at some point started swapping, which will make things *very* slow. 

Best regards, 
-Salvador. 

----- Original Message ----- 
From: "Mingsu Si" <mingsusi at gmail.com> 
To: smeagol-discuss at lists.tchpc.tcd.ie 
Sent: Thursday, December 4, 2008 4:23:41 AM GMT -05:00 US/Canada Eastern 
Subject: [Smeagol-discuss] stay for a long time when running the transport calculations! 

Dear all, 

When I run the transport calculations, the program stay for a long time at the the following step. What's the possible problem about it? 
Any information are welcome. 

sims 



------------------------------------------------------------------------------------------------ 
siesta: 3.64339 9.66028 52.14890 1 147 
siesta: 3.05380 0.73510 49.84533 1 148 
siesta: 1.80091 5.98288 49.81887 1 149 
siesta: 1.59871 4.60337 52.16969 1 150 
siesta: 5.14006 -1.04691 49.85855 1 151 
siesta: 6.40050 -1.63650 52.19993 1 152 
siesta: 2.26200 1.91618 52.18292 1 153 
siesta: 10.49932 -1.41163 49.85100 1 154 
siesta: 9.15384 -1.81036 52.20182 1 155 
siesta: 12.81802 0.03402 49.84911 1 156 
siesta: 13.77611 1.06014 52.19615 1 157 
siesta: 14.83247 3.60938 52.19048 1 158 

initatomlists: Number of atoms, orbitals, and projectors: 158 2006 2486 

siesta: System type = chain 

* Maximum dynamic memory allocated = 3 MB 

siesta: =============================== 
SMEAGOL Bias step = 0, V = 0.000 Ry 
Begin CG move = 0 
=============================== 

InitMesh: MESH = 128 x 128 x 240 = 3932160 
InitMesh: Mesh cutoff (required, used) = 200.000 205.308 Ry 

* Maximum dynamic memory allocated = 1085 MB 
gensvd: Leads decimation 
gensvd: Dim of H1 and S1 : 520 
gensvd: Rank of H1: 57 
gensvd: Rank of (H1,S1): 217 
gensvd: Decimated states: 246 
gensvd: Decimation from the right 
gensvd: Leads decimation 
gensvd: Dim of H1 and S1 : 520 
gensvd: Rank of H1: 57 
gensvd: Rank of (H1,S1): 217 
gensvd: Decimated states: 246 
gensvd: Decimation from the right 
----------------------------------------------------------------------------------------------------- 


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