[sharp-discuss] Autosharp- CAD problem
Clemens Vonrhein
vonrhein@globalphasing.com
Fri, 30 Jan 2004 08:16:50 +0000
Dear Sam,
there are two variables within a CCP4 setup related to scratch space:
$CCP4_SCR and $BINSORT_SCR. When installing SHARP/autoSHARP (or adding
new machines to an existing installation) the values are taken from
your current environment or previous setups. It looks like there is
something wrong with these settings:
- maybe these directories don't even exist? The 'normal' CCP4 setup
sets e.g. CCP4_SCR=/tmp/$USER. However, some systems clear out
/tmp regularly, deleting even subdirectories. Therefore, this
directory might not exist.
- maybe the directory BINSORT_SCR and/or CCP4_SCR is pointing to is
not large enough?
So the checks yo should make:
1. what are the settings of these variables on the various machines
you have:
% cd /where/ever/sharp
% grep "_SCR=" machines/*/ccp4.setup
which will tell you for each machine (i.e. subdirectory within
$BDG_home/machines) the values.
2. make sure these directories actually exist (ON THAT PARTICULAR
MACHINE!) and will keep existing even after a while.
3. make sure they have enough free space (maybe clear out a few old
stuff or enlarge them).
A final solution is to create a scratch directory within the
SHARP/autoSHARP installation (which is visible on all machines anyway)
that has enough space:
% cd /where/ever/sharp
% mkdir scratch
==> set CCP4_SCR and BINSCORT_SCR to /where/ever/sharp/scratch in
all machines/*/ccp4.setup files
==> BUT: if this disk is NFS mounted some operations (like e.g. CAD)
might be significantly slower than if it was a truly local disk like
/tmp.
Hope that helps
Cheers
Clemens
On Thu, Jan 29, 2004 at 11:34:48PM -0000, Arulandu, Arockiasamy wrote:
>
> Hi all,
>
>
> here is the problem when I try to Run Autosharp:
>
>
> Autosharp stops at while converting files. I found the error message in
>
> in the log file: CAD_w1.log
>
>
> i could find two eooer messages:
>
> 1: * Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
>
> 1 unknown /
> unknown012704:23:11:55
> 66.8340 66.8340 binsort -- I/O error (check space available in
> $BINSORT_SCR): No such file or directory
>
> 2: CAD failed to release record to sort procedure, stat CAD: Fatal Error
> us = 32
>
> CAD: Fatal Error
> Times: User: 0.3s System: 0.0s Elapsed: 0:00
>
>
>
> could somebody tell me what is really wrong here? I have attached the CAD log
> file here, if some one interested to look at it.
>
> thanks a lot.
>
> sam
>
>
>
>
> 1###############################################################
> ###############################################################
> ###############################################################
> ### CCP4 4.2: CAD version 4.2 : 25/01/02##
> ###############################################################
> User: Run date: 1/27/04 Run time:23:12:02
>
>
> Please reference: Collaborative Computational Project, Number 4. 1994.
> "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
>
> as well as any specific reference in the program write-up.
>
>
> Data line--- LABI FILE 1 E1=Fw1 E2=SIGFw1 E3=DANOw1 E4=SIGDANOw1 E5=ISYMw1
> Data line--- OUTL SPACE P6522
>
> FORMATTED OLD file opened on unit 24
> Logical name: SYMOP, Filename: /yusr/pomp/sharp3/database/symop
>
> Data line--- SYMM P6522
>
> FORMATTED OLD file opened on unit 24
> Logical name: SYMOP, Filename: /yusr/pomp/sharp3/database/symop
>
> Data line--- SORT HKL SORT LKH
> Data line--- END
> No CTYP lines input for file: 1
> Indices output even if all data items flagged "missing"
> Warning, NOT all LABOUT data lines given
>
> (Q)QOPEN: file opened on unit 1 Status: READONLY
> Logical Name: HKLIN1 Filename: CONVERT/TRUNCATE_w1.mtz
>
> HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
>
> * Title:
>
> From Truncate on the 1/27/04.
>
> * Number of Datasets = 1
>
> * Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
>
> 1 unknown /
> unknown012704:23:11:55
> 66.8340 66.8340 166.7070 90.0000 90.0000 120.0000
>
>
> * Number of Columns = 18
>
> * Number of Reflections = 17971
>
> * Missing value set to NaN in input mtz file
>
> * Column Labels :
>
> H K L Fw1 SIGFw1 DANOw1 SIGDANOw1 F(+) SIGF(+) F(-) SIGF(-) IMEAN SIGIMEAN I(+)
> SIGI(+) I(-) SIGI(-) ISYMw1
>
> * Column Types :
>
> H H H F Q D Q G L G L J Q K M K M Y
>
> * Associated datasets :
>
> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
>
> * Cell Dimensions :
>
> 66.8340 66.8340 166.7070 90.0000 90.0000 120.0000
>
> * Resolution Range :
>
> 0.00093 0.27699 ( 32.791 - 1.900 A )
>
> * There is no sort order recorded in the MTZ header
>
> * Space group = P6522 (number 179)
>
>
> Reciprocal space symmetry
> Space group: P6522 (179) Point group: 622 Laue group: 6/mmm
> Asymmetric unit: [6/mmm] hkl:h>=0, k>=0, l>=0 with h>=k
>
> Original indices for reflection hkl with symmetry number ISYM
>
> Bijvoet positive
> ISYM ISYM ISYM ISYM
> ISYM 1 +h,+k,+l 7 -h,-k,+l 13 +k,+h,-l 19 -k,-h,-l
> ISYM 3 -h-k,+h,+l 9 +h+k,-h,+l 15 +h,-h-k,-l 21 -h,+h+k,-l
> ISYM 5 +k,-h-k,+l 11 -k,+h+k,+l 17 -h-k,+k,-l 23 +h+k,-k,-l
>
> Bijvoet negative
> ISYM ISYM ISYM ISYM
> ISYM 2 -h,-k,-l 8 +h,+k,-l 14 -k,-h,+l 20 +k,+h,+l
> ISYM 4 +h+k,-h,-l 10 -h-k,+h,-l 16 -h,+h+k,+l 22 +h,-h-k,+l
> ISYM 6 -k,+h+k,-l 12 +k,-h-k,-l 18 +h+k,-k,+l 24 -h-k,+k,+l
>
>
>
> Chosen Asymmetric unit of reciprocal space:
> [6/mmm] hkl:h>=0, k>=0, l>=0 with h>=k
>
>
> ** "Missing" flag set in HKLIN1 to Nan:
>
>
> ** "Missing" entries LISTED as -999.000
>
>
> After Processing File_Number: 1
> Number of columns so far : 8
> Accummulated Out_Put_MTZ_labels are:
> E11=Fw1 E21=SIGFw1 E31=DANOw1 E41=SIGDANOw1
> E51=ISYMw1
>
>
> MTZOUT_LABELS are H K L S and -
> Fw1 SIGFw1 DANOw1 SIGDANOw1
> ISYMw1
> 1 sort keys, in columns 1
>
>
>
>
>
> (Q)QOPEN: file opened on unit 1 Status: READONLY
> Logical Name: HKLIN1 Filename: CONVERT/TRUNCATE_w1.mtz
>
> HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 2
>
> * Title:
>
> From Truncate on the 1/27/04.
>
> * Number of Datasets = 1
>
> * Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
>
> 1 unknown /
> unknown012704:23:11:55
> 66.8340 66.8340 binsort -- I/O error (check space available in
> $BINSORT_SCR): No such file or directory
> 166.7070 90.0000 90.0000 120.0000
>
>
> * Number of Columns = 18
>
> * Number of Reflections = 17971
>
> * Missing value set to NaN in input mtz file
>
> * Column Labels :
>
> H K L Fw1 SIGFw1 DANOw1 SIGDANOw1 F(+) SIGF(+) F(-) SIGF(-) IMEAN SIGIMEAN I(+)
> SIGI(+) I(-) SIGI(-) ISYMw1
>
> * Column Types :
>
> H H H F Q D Q G L G L J Q K M K M Y
>
> * Associated datasets :
>
> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
>
> * Cell Dimensions :
>
> 66.8340 66.8340 166.7070 90.0000 90.0000 120.0000
>
> * Resolution Range :
>
> 0.00093 0.27699 ( 32.791 - 1.900 A )
>
> * There is no sort order recorded in the MTZ header
>
> * Space group = P6522 (number 179)
>
> * Input Program Labels :
>
> H K L E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12 E13 E14 E15 E16 E17 E18 E19 E20 E21
> E22 E23 E24 E25 E26 E27 E28 E29 E30 E31 E32 E33 E34 E35 E36 E37 E38 E39 E40 E41
> E42 E43 E44 E45 E46 E47 E48 E49 E50 E51 E52 E53 E54 E55 E56 E57 E58 E59 E60 E61
> E62 E63 E64 E65 E66 E67 E68 E69 E70 E71 E72 E73 E74 E75 E76 E77 E78 E79 E80 E81
> E82 E83 E84 E85 E86 E87 E88 E89 E90 E91 E92 E93 E94 E95 E96 E97 E98 E99 E100
> E101 E102 E103 E104 E105 E106 E107 E108 E109 E110 E111 E112 E113 E114 E115 E116
> E117 E118 E119 E120 E121 E122 E123 E124 E125 E126 E127 E128 E129 E130 E131 E132
> E133 E134 E135 E136 E137 E138 E139 E140 E141 E142 E143 E144 E145 E146 E147 E148
> E149 E150 E151 E152 E153 E154 E155 E156 E157 E158 E159 E160 E161 E162 E163 E164
> E165 E166 E167 E168 E169 E170 E171 E172 E173 E174 E175 E176 E177 E178 E179 E180
> E181 E182 E183 E184 E185 E186 E187 E188 E189 E190 E191 E192 E193 E194 E195 E196
> E197
>
> * Input File Labels :
>
> H K L Fw1 SIGFw1 DANOw1 SIGDANOw1 F(+) SIGF(+) F(-) SIGF(-) IMEAN SIGIMEAN I(+)
> SIGI(+) I(-) SIGI(-) ISYMw1
>
> * Lookup Table : the number indicates the input column no.
> * Array element n corresponds to the nth program label
>
> 1 2 3 4 5 6 7 18 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0
>
>
> Reading from HKLIN mtz file_Number = :1
> This file written with MTZLIB Version Number : MTZ:V1.1
> File HKLIN1 contains a total of 18 Columns
> and a total of 17971 Reflections
> ****** EPSILON ZONES - Reflection Classes and their multiplicity ******
> EPSILON Zone 1
> Reflections of type h00
> Multiplicity 2
> EPSILON Zone 2
> Reflections of type 0k0
> Multiplicity 2
> EPSILON Zone 3
> Reflections of type 00l
> Multiplicity 6
> EPSILON Zone 4
> Reflections of type hh0
> Multiplicity 2
> EPSILON Zone 5
> Reflections of type h -h0
> Multiplicity 2
> EPSILON Zone 6
> Reflections of type -h 2h 0
> Multiplicity 2
> EPSILON Zone 7
> Reflections of type 2h -h 0
> Multiplicity 2
> EPSILON Zone 8
> Reflections of type hkl
> Multiplicity 1
> Centric Zone 1 Reflections of Type 0kl
> Centric Zone 2 Reflections of Type h0l
> Centric Zone 3 Reflections of Type hk0
> Centric Zone 4 Reflections of Type hhl
> Centric Zone 5 Reflections of Type h -hl
> Centric Zone 6 Reflections of Type -h 2h l
> Centric Zone 7 Reflections of Type 2h -h l
> CAD failed to release record to sort procedure, stat CAD: Fatal Error
> us = 32
>
> CAD: Fatal Error
> Times: User: 0.3s System: 0.0s Elapsed: 0:00
>
> ------------------------------------------------
>
>
>
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--
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
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