Old News and Bugs

Old News

Java based Web

A version of Web written in Java by Dr. Bimal Rath is available for Linux, and for Windows. This cross platform package for 'Visualization and Analysis of SPIDER Images' may eventually be upgraded to encompass most all of the capabilities of the current X-window based Web.

SPIDER for HP/Compaq/Digital Alpha with True64 Unix

We have discontinued providing SPIDER executables and precompiled libraries for True64 Unix as our Alpha systems have retired. We still will provide Makefiles which can be used to compile SPIDER on your own system.

Obsolete Features in SPIDER

The use of continuation lines in SPIDER document files, the assigned meanings for system registers 1...8, and the old formalism for filename substitution have removed in recent release of SPIDER. The very old formalism for procedure file names <letter><letter><digit> will be removed in next release of SPIDER. After that all procedure invocations must start with an "@" sign

Irix 5.3 executable phased out.

Since we do not have a F90 compiler which can create "mips2" code we are unable to supply new versions of SPIDER for use on SGI machines running Irix 5.*.

SPIDER format now in SGI's Image Format Library (IFL) .

SGI has released software for accessing SPIDER format files under their Imagevision software (e.g. imgworks, imgcopy, etc.)

Old Bugs

RF & RF 3

--> present. NX must be equal to NY for correct answers.

10/10/01 AL

RT 90

--> present. The 'RT 90' operation reforms an image's columns and rows (or just rows for 180 degrees). The action of such a rotation is not the same as other "RT" rotations since the center of rotation differs and object handedness can be altered. Thus 'RT 90' is not interchangeable with other 'RT' operations.

11/27/98 AL

PW

On some 64 bit SGI machines with 7.3.13m FORTRAN, SPIDER encounters a bad memory leak.

Install SGI patch 4511 (7.3 FORTRAN runtime #3 for IRIX 6.5) to fix this. (We have introduced a "work-around" which avoids most of the leak.)

8/14/02 AL

CA S

June 2001 --> Feb. 2002 (version 8.02). With small problems the Coran option used the wrong formulation and never finished processing.

8/14/02 AL

RF & RF 3

--> present. NSAM must be equal to NROW for correct answers.

10/10/01 AL

Integers larger than 99999 are incorrect when placed in doc files.

?--> Aug. 2000 (version 6.34). Numbers in document files were stored with G12.5 Fortran format so that integers greater than 99999 lack precision. As of version 6.35 integers > 999999 show the same "error" but integers < 999999 can be used OK. Keeping precise integers > 999999 in a document file will require major changes in SPIDER document files. This will be done in a subsequent release.

8/22/00 AL

Inline Stack File Memory Leak

?-->present. SPIDER has a memory leak on SGI Irix 6.5 which sometimes occurs when one alternately creates and deletes an inline stack file. We have introduced a workaround which will lessen the occurance.

10/10/99 AL

FT, AC, and CC

--> present. SGI's version of "libblas" routines have a slow memory leak in routines necessary for Fourier transforms. When performing these operations millions of times in a single run you may exhaust system memory and SPIDER may crash. SGI acknowledges a problem, and suggests that users switch to the "CRAY Subroutine Library" which is not included with the Irix OS, which we are reluctant to use.
We have introduced a work-around that minimizes the effect of this bug under most circumstances. Details.

3/20/99 AL

Competing SPIDER parallel jobs on Compaq Alpha mutiprocessor machines sometimes show extremely poor performance.

To overcome this problem set the MP_SPIN_COUNT environmental variable to a lower number such as 5000 before starting the second such job. Under the "C" shell this can be done like this: setenv MP_SPIN_COUNT 5000
This may decrease performance if there is only a single such job so do not use this unless needed. Details

5/26/00 AL

Sometimes parallel jobs on SGI Irix 6.5 get bad priority.

Under Irix 6.5 the scheduler for parallel threads sometimes seems to misbehave. To overcome this problem we set the MPC_GANG environmental variable ON before running SPIDER (under "C" shell this can be done like this: setenv MPC_GANG ON
This activates an older scheduling protocol that seems to work better.
Some users have reported that setting the "OMP_DYNAMIC" environment variable to "FALSE" improves scheduling problems on their SGI multi-processor machines. setenv OMP_DYNAMIC FALSE

4/10/00 AL

PW

On some 64 bit SGI machines with 7.3.1.3m FORTRAN, SPIDER encounters a bad memory leak.

Install SGI patch 4511 (7.3 FORTRAN runtime #3 for IRIX 6.5) to fix this. (We have introduced a "work-around" which avoids most of the leak.)

8/14/02 AL

RR

?--> Nov. 2001 (version 7.09). When a register from a higher level procedure is specified for a Value, register content from current procedure is used instead.

11/19/01 AL

DO

?--> Nov. 2001 (version 7.09). Comments (;) on a DO LB.... line cause loop to fail.

11/19/01 AL

Use of ?xxxxx? in procedures.

Aug. 2000 -> (version 7.01). Using ?*****? for interactive symbolic parameter entry after operations other than 'FR' fails. Workaround: use 'FR' to extablish symbolic parameters.

2/27/01 AL

Object size was wrong in AP SR

Operation would crash if object size was requested which was more than half the reconstruction size.

?--> Feb. 2001 (Fixed in version 7.00).

2/08/01 AL

Operation BP RP crashes on Compaq Alpha systems (OK on SGI).

Dec 1999?--> May. 2000 (version 6.26).( Fixed in release 6.28)

8/22/00 AL

Operation CP FROM MRC sometimes creates empty file.

Dec 1999?--> May. 2000 (version 6.28). Fixed in most recent release (6.30)

5/26/00 AL

Can not open stack files for both input and output.

?-->Feb 2001. Data files can not be opened for both input and simultaneous output. This mainly affects operations on images kept within the same physical stack file. The images must be in different stacks. This problem has been fixed in release 7.0.

2/22/00 AL

DO, DO LOOPS

1996?--> Aug. 1999 (version 6.12). Do loop stacking was handled incorrectly requiring that some input values had to be enclosed in ()'s even when there was no local DO-LOOP. This has been fixed.

8/17/99 AL

DO

???? --> 10/21/98 When a nested do loop having a single label digit and a comment following the label exits the inner loop early via a "GO TO", the outer loop does not finish.
Workaround: remove comment from outer loop label.

10/20/98 AL

AD, MU& SU

???? --> 08/21/98 the "AD", "MU" & "SU" operations did not work properly for serial summation (multiplication or subtraction) following the third file. Under certain circumstances SPIDER would appear to be summing the files but the sum was NOT written into the output file.

08/16/98 AL

AP MQ

01/4/97 --> 07/16/97 the "AP MQ" operation did not work properly for EVEN image dimensions. It worked properly for ODD image dimensions.

07/16/97 PP

image header problem

06/96 --> 02/97 certain SPIDER images created with this release of SPIDER give a nonsense error message when accessed:
*** THIS IMAGE FROM STACK NO LONGER IN USE
See the FAQ for a method of fixing these files.

05/15/97 AL

CL KM

--> 07/25/97 the "CL KM" operation did not give correct results.

08/25/97 PP

{***X??} strings

06/29/97 --> 11/20/97 passing of {***X??} strings to procedures resulted in an incorrect binding time.

11/22/97 AL

CP FIX

--> 12/10/97 some stack files have wasted space following overall file header.

12/08/97 al