From jillian.maddox alumni.unimelb.edu.au Thu Apr 11 21:15:29 2013
From: Jill Maddox <jillian.maddoxalumni.unimelb.edu.au>
To: Multiple Recipients of <crimap-usersanimalgenome.org>
Subject: Re: Error information
Date: Thu, 11 Apr 2013 21:15:29 -0500
Hi Gang and others
In build CRI-MAP works by trying to insert new markers into existing maps.
Previously when a calculation required too much memory it crashed without
giving any information as to what the problem was. We have adjusted CRI-MAP
so that when it asks for too much memory for a likelihood calculation or
the time taken for the likelihood calculation is likely to be excessive
(based on number of individual calculations needed to handle the switches
for the order and test marker) then the calculation is skipped and put into
the output. The logging of the information enables you to see which map
orders haven't been calculated and what the number of calculations is.
There are some values you can adjust in the defs.h file HIGH_MEMORY_SIZE
default is 2000000000LL MAX_PRODUCT_CALCS default is 500000000LL
HIGH_MEMORY_BITS default is 25
If a map order requires too many calculations and consequently too much
memory then you won't be able to add other markers to a map it so it is
best to leave these markers to last.
Regards
Jill
At 08:59 AM 12/04/2013, Li, Gang wrote:
>Dear Jill:
>
> When I run cirmap , Build, I got some information like these:
>
>alloc_srec_pos: Memory bits requested = 24.
>Current marker order:
>736 1345 1327 1280 1245 1202 1188 1167 1147 1092 1062 917 1019 992
>939 895 893 783 741 728 723 692 682 659 616 484 428 403 380 308 287
>244 208 178 230 159 150 129 16
>alloc_srec_pos: Required product calculations 2426230968 too high for order:
>736 1345 1327 1280 1245 1202 1188 1167 1147 1092 1062 1019 917 992
>939 895 893 783 741 728 723 692 682 659 616 484 428 403 380 308 287
>244 208 178 230 159 150 129 16
>alloc_srec_pos: Abandoning this order.
>mle: Skipping calculation of order
>Warning: Zero likelihood for order:
>736 1345 1327 1280 1245 1202 1188 1167 1147 1092 1062 1019 917 992
>939 895 893 783 741 728 723 692 682 659 616 484 428 403 380 308 287
>244 208 178 230 159 150 129 16
>alloc_srec_pos: Required product calculations 1573477612 too high for order:
>736 1345 1327 1280 1245 1202 1188 1167 1147 1092 1062 1019 992 917
>939 895 893 783 741 728 723 692 682 659 616 484 428 403 380 308 287
>244 208 178 230 159 150 129 16
>alloc_srec_pos: Abandoning this order.
>mle: Skipping calculation of order
>Warning: Zero likelihood for order:
>736 1345 1327 1280 1245 1202 1188 1167 1147 1092 1062 1019 992 917
>939 895 893 783 741 728 723 692 682 659 616 484 428 403 380 308 287
>244 208 178 230 159 150 129 16
>alloc_srec_pos: Required product calculations 5380535471 too high for order:
>736 1345 1327 1280 1245 1202 1188 1167 1147 1092 1062 1019 992 939
>917 895 893 783 741 728 723 692 682 659 616 484 428 403 380 308 287
>244 208 178 230 159 150 129 16
>alloc_srec_pos: Abandoning this order.
>mle: Skipping calculation of order
>Warning: Zero likelihood for order:
>736 1345 1327 1280 1245 1202 1188 1167 1147 1092 1062 1019 992 939
>917 895 893 783 741 728 723 692 682 659 616 484 428 403 380 308 287
>244 208 178 230 159 150 129 16
>alloc_srec_pos: Memory bits requested = 21.
>Current marker order:
>736 1345 1327 1280 1245 1202 1188 1167 1147 1104 1092 1062 1019 992
>939 895 893 783 741 728 723 692 682 659 616 484 428 403 380 308 287
>244 208 178 230 159 150 129 16
>alloc_srec_pos: Memory bits requested = 20.
>Current marker order:
>736 1345 1327 1280 1245 1202 1188 1167 1147 1092 1104 1062 1019 992
>939 895 893 783 741 728 723 692 682 659 616 484 428 403 380 308 287
>244 208 178 230 159 150 129 16
>alloc_srec_pos: Memory bits requested = 21.
>
>
>Because I am running a big SNP matrices to test and build a linkage
>map, I guess may be the parameters in file defs.h which need to be
>changed fit my data. Do you have any good suggestion for that?
>
>I tried some changes of NUM_LOCI and MAX_NUM_SWITCHS. I only tested
>these and recompile crimap. I don't know how to make a more
>appropriate adjustments of parameters. Can I ask help from you?
>
>Thank you very much.
>
>Best regards,
>Gang
***************************************************************
Jill Maddox 16 Park Square Port Melbourne, 3207 Australia phone: 03 9646
0428 E-mail: jillian.maddoxalumni.unimelb.edu.au
***************************************************************
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