Re: [ccp4bb] seeking help from a bioinformatics guru

[Matthew Bowler]

this website from Stephen White's lab is has many of the details you are 
looking for, best wishes, Matt.


http://blanco.biomol.uci.edu/mpstruc/listAll/list




On 07/03/2013 08:10, Mike John wrote:

Hi, all,

Would anybody help me out there? I'd like to got the statistics about:
1, How many unique transmemberane  protein structure have by far been 
solved by X-ray?
2, How many X-ray structures of water-soluble domains in which their 
membrane-anchoring alpha helices have been removed?


I tried PDB search and PDBe search, but no success by far?

Thank you very much!

Mike



--
Matthew Bowler
Synchrotron Science Group
European Molecular Biology Laboratory
BP 181, 6 rue Jules Horowitz
38042 Grenoble Cedex 9
France
===
Tel: +33 (0) 4.76.20.76.37
Fax: +33 (0) 4.76.88.29.04

http://www.embl.fr/
===

[ccp4bb] seeking help from a bioinformatics guru

[Mike John]

Hi, all,

Would anybody help me out there? I'd like to got the statistics about:
1, How many unique transmemberane  protein structure have by far been solved by 
X-ray?
2, How many X-ray structures of water-soluble domains in which their 
membrane-anchoring alpha helices have been removed?

I tried PDB search and PDBe search, but no success by far?

Thank you very much!

Mike

  

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

[Ed Pozharski]

Thierry,

I ran both versions on the same input file and numerical results are 
essentially the same.  After 10 cycles of refinement the r.m.s.d. 
between two models produced with different versions is <0.0004A.  
Basically, about 5% of coordinates differ in the last digit (i.e. by 
0.001A).  Frankly, I expected results to be exactly identical, but the 
difference is too small to be of concern, imho.


Cheers,

Ed.

On 03/04/2013 10:19 AM, Fischmann, Thierry wrote:

Ed,

Are the numerical results the same ? Not likely that there is a problem. But if 
you haven't done it already it is worth checking by running the tests provided 
with the suite. Aggressive optimization can be a source of bugs.

Best regards
Thierry

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed 
Pozharski
Sent: Monday, March 04, 2013 8:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote:

Running times were, correspondingly, 32.2s, 35.1s and 18.7s.


Numbers are almost too impressive to believe :)

How does it compare with ifort (which I thought should be the fastest
option on intel processors and thus unavailable (not free) for most DIY
compilation given licensing issues)?




--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[Francois Berenger]

Hi,

The command:
$ aptitude install fort77
would install an f77 command on Ubuntu/Debian Linux.
In fact that's a wrapper for f2c, but maybe it behaves like
a real f77 compiler, I would give it a try personnally.

On 03/06/2013 06:48 PM, vellieux wrote:

Hello,

For those who still know the Fortran language and its Fortran 77
variant, I used to have a g77 compiler here (Linux box), and now on the
new box it's no longer g77 but gfortran.

When compiling Fortran77 code (these are the flags used for compilation:
-o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double
-funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the
libraries on that same compile line)

I get errors (at run time) of the type:

At line 138 of file program.f (unit = 6, file = 'stdout')
Fortran runtime error: Missing initial left parenthesis in format

When looking at this code (which compiled perfectly well using g77 - I
removed the flag "-fno-globals" which doesn't seem to exist any more in
gfortran) the Fortran code that I see appears to have all parentheses in
the correct places.

Any idea of what must be done with existing Fortran 77 code in order to
get it to compile and run with gfortran ? Otherwise any idea which
compiler should be used to compile Fortran 77 code ?

Thanks in advance,

Fred.

[ccp4bb] Job Posting: US East Coast Mosquito Crystallization Robot Sales Representative

[Soheila Vaezeslami]

*Location: East Coast, USA (telecommuting OK)*
*Type: Full-time*
*Experience: Associate*
*Functions: Sales*
*Industries: Biotechnology*
*Compensation: Salary, Commission, & Benefits*
*
*
*Please RSVP to casey.car...@ttplabtech.com*

*Job Description*

TTP Labtech is currently seeking an enthusiastic and motivated candidate to
fill the US East Coast Sales Representative position.
The qualified candidate will be an integral part of the sales team. He/she
will be responsible for selling state-of-the-art liquid handling
instrumentation used within structural biology and molecular biology
research areas.
This work includes (but is not limited to) building a sales pipeline for a
diverse range of products, understanding a complex capital equipment sales
cycle, developing strong customer relationships and ensuring complete
customer service and satisfaction from beginning to end. Also working
alongside the marketing and support team(s), the successful candidate must
be team oriented

*Desired Skills & Experience*
Essential job functions and responsibilities will include:
 Selling capital equipment (including a range of products, warranties, and
consumable items)
 Building a sales pipeline for the product range
 Understanding and keeping-up with the sales cycle process
 Building relationship with existing customer base
 Conducting product demos for customers
 Travelling extensively along the East Coast territory
 Establishing collaborative relationships with academic partners,
businesses, and the like.
 Reporting competitive intelligence
 Developing methodologies and unique strategies for competitive sales
 Ensuring proper customer satisfaction & customer service (working with
the support team)
 Developing awareness campaigns for the complete range of products &
consumables (alongside the marketing team)
 Designing incentive programs to engage customers (working alongside the
marketing team)
 Maintaining Salesforce.com database

*Qualifications:*
 Bachelor’s degree required (in biological science highly favored)
 Comprehensive understanding of protein crystallography required
 Experience with PCR applications preferred
 Familiarity with the concepts of liquid handling preferred
 2-3+ years capital equipment sales experience
 CRM data entry experience (Salesforce.com preferred)
 Sound computer skills and use of MSOffice applications, etc.
 Highly personable with demonstrated customer relations skills
 Excellent verbal & written communication skills are necessary
 Ability to prioritize and multi-task; will handle multiple projects
simultaneously
 Strong organizational and time management skills
 Ability to work independently is a must
 Demonstrate a high degree of personal and professional integrity in all
interactions with internal and external stakeholders

*Company Description*
TTP Labtech has firmly established itself as a global developer and
manufacturer of high quality, robust and innovative automated laboratory
equipment for both the academic and industrial sectors of pharmaceutical
and biotech research.
TTP Labtech offers a portfolio of products that minimize assay volumes,
reduce material handling costs and put the discovery tools back in the
hands of the scientist. With new products in the pipeline, our strength
comes from the ability to combine cutting edge science with first-rate
engineering, enabling us to design and develop unique and novel products.
To learn more about TTP Labtech Ltd, a TTP Group plc company visit:
www.ttplabtech.com

Re: [ccp4bb] Way off topic: Donate V. Cholera Genomic DNA?

[Jacob Keller]

Dear All, thanks very much for the various suggestions--I finally made the
connection. A good point was also made that gene synthesis is becoming ever
cheaper (~$0.28/bp) so maybe PCRing from genomic DNA is not always
advisable. I'll keep this in mind for the future, although for this one I
had my reasons for going for the gDNA.

Thanks again,

Jacob

On Tue, Mar 5, 2013 at 1:07 PM, Jacob Keller  wrote:

> Dear List,
>
> please pardon the major off-topicity, but I need a trace amount of V
> cholera genomic DNA to PCR from, and it just kills me to spend ~$300 to
> order it for this one and only use. Is anyone in the DC/Baltimore area
> willing and able to donate this? I travel on the capitol beltway daily, so
> anything nearby would work, esp. NIH.
>
> Jacob
>
> --
> ***
> Jacob Pearson Keller, PhD
> Postdoctoral Associate
> HHMI Janelia Farms Research Campus
> email: k ell...@janelia.hhmi.org
> ***
>



-- 
***
Jacob Pearson Keller, PhD
Postdoctoral Associate
HHMI Janelia Farms Research Campus
email: k ell...@janelia.hhmi.org
***

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

[Ed Pozharski]

On 03/04/2013 10:02 AM, Marcin Wojdyr wrote:

It also puzzled me, but I haven't done more careful benchmarking yet.
What did you get after compiling refmac?


My numbers are not as impressive, but I also get quite detectable 
improvement, from 35s to 27s (ccp4-6.3.0 vs compiled from source). This 
is with gcc-4.6 though.  Importantly, both binaries are the *same* 
version of refmac, 5.7.0032.


--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs

Re: [ccp4bb] SOLVED [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[vellieux]

Hi again Ian and "list",

The following flags seem to work fine:
gfortran -o ../bin/$1 -std=legacy -ffixed-format -Wno-globals -w -O3 
-funroll-loops -ffast-math -fno-second-underscore $1.f (followed by the 
library or libraries, compiled with the same flags).


Problem solved as far as I am concerned (until there is yet another 
compiler I guess, next Linux box down the road).


Fred.

On 06/03/13 13:55, Ian Tickle wrote:
Fred, OK I just noticed I didn't have the  -malign-double flag.  With 
that it compiles but on running I get:


Program received signal SIGSEGV: Segmentation fault - invalid memory 
reference.


Backtrace for this error:
#0  0x12244B
#1  0x122A9C
#2  0x473907
#3  0x1BD238
#4  0x1CB4BF
#5  0x80486E2 in MAIN__
Segmentation fault

Without that flag it compiles & runs without error.  So you may want 
to try it just without that flag.


Cheers

-- Ian


--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] SOLVED [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[Ian Tickle]

Fred, OK I just noticed I didn't have the  -malign-double flag.  With that
it compiles but on running I get:

Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.

Backtrace for this error:
#0  0x12244B
#1  0x122A9C
#2  0x473907
#3  0x1BD238
#4  0x1CB4BF
#5  0x80486E2 in MAIN__
Segmentation fault

Without that flag it compiles & runs without error.  So you may want to try
it just without that flag.

Cheers

-- Ian



On 6 March 2013 12:33, vellieux  wrote:

> Hi all,
>
> Problem solved thanks to Jorge Navaza's suggestion: remove all compilation
> flags but only have -Wall as a compilation flag.
>
> There is no run time error any more and there is no error at compilation
> time. The program runs fine.
>
> Thanks to Thomas Jens, Harry Powell, Ian Tickle, Ian Clifton and Bernhard
> Rupp for their suggestions.
>
> Fred.
>
> On 06/03/13 10:48, vellieux wrote:
>
>> Hello,
>>
>> For those who still know the Fortran language and its Fortran 77 variant,
>> I used to have a g77 compiler here (Linux box), and now on the new box it's
>> no longer g77 but gfortran.
>>
>> When compiling Fortran77 code (these are the flags used for compilation:
>> -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double -funroll-loops
>> -ffast-math -fno-second-underscore $1.f , followed by the libraries on that
>> same compile line)
>>
>> I get errors (at run time) of the type:
>>
>> At line 138 of file program.f (unit = 6, file = 'stdout')
>> Fortran runtime error: Missing initial left parenthesis in format
>>
>> When looking at this code (which compiled perfectly well using g77 - I
>> removed the flag "-fno-globals" which doesn't seem to exist any more in
>> gfortran) the Fortran code that I see appears to have all parentheses in
>> the correct places.
>>
>> Any idea of what must be done with existing Fortran 77 code in order to
>> get it to compile and run with gfortran ? Otherwise any idea which compiler
>> should be used to compile Fortran 77 code ?
>>
>> Thanks in advance,
>>
>> Fred.
>>
>>
>
> --
> Fred. Vellieux (B.Sc., Ph.D., hdr)
> ouvrier de la recherche
> IBS / ELMA
> 41 rue Jules Horowitz
> F-38027 Grenoble Cedex 01
> Tel: +33 438789605
> Fax: +33 438785494
>

Re: [ccp4bb] SOLVED [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[vellieux]

Hi all,

Problem solved thanks to Jorge Navaza's suggestion: remove all 
compilation flags but only have -Wall as a compilation flag.


There is no run time error any more and there is no error at compilation 
time. The program runs fine.


Thanks to Thomas Jens, Harry Powell, Ian Tickle, Ian Clifton and 
Bernhard Rupp for their suggestions.


Fred.

On 06/03/13 10:48, vellieux wrote:

Hello,

For those who still know the Fortran language and its Fortran 77 
variant, I used to have a g77 compiler here (Linux box), and now on 
the new box it's no longer g77 but gfortran.


When compiling Fortran77 code (these are the flags used for 
compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 
-malign-double -funroll-loops -ffast-math -fno-second-underscore $1.f 
, followed by the libraries on that same compile line)


I get errors (at run time) of the type:

At line 138 of file program.f (unit = 6, file = 'stdout')
Fortran runtime error: Missing initial left parenthesis in format

When looking at this code (which compiled perfectly well using g77 - I 
removed the flag "-fno-globals" which doesn't seem to exist any more 
in gfortran) the Fortran code that I see appears to have all 
parentheses in the correct places.


Any idea of what must be done with existing Fortran 77 code in order 
to get it to compile and run with gfortran ? Otherwise any idea which 
compiler should be used to compile Fortran 77 code ?


Thanks in advance,

Fred.




--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

[ccp4bb] Postdoctoral opportunity

[Colin Levy]

Dear BB,
Please see details below of a PDRA position available at the University of 
Manchester in the laboratory of Dr Lydia Tabernero. All enquiries should be 
directed to Dr Tabernero and not myself please.

lydia.tabern...@manchester.ac.uk

Many thanks,

Colin

Postdoctoral Position in X-ray Crystallography

Structure of the endosomal ESCRT-I core complex

Faculty of Life Sciences, University of Manchester
Manchester, UK

A postdoctoral position is available in the laboratory of Dr Lydia Tabernero to 
study the structural basis for the assembly of a protein complex that is 
essential for mitogenic receptor down regulation. The project will focus on 
understanding the core structure of the endosomal-sorting complex, ESCRT-I 
(Stefani et al., 2011, Curr. Biol. 21, 1245050).
The position is part of an ongoing research collaboration between Dr Lydia 
Tabernero and Professor Philip Woodman directed towards understanding the 
molecular basis for the down-regulation of the epidermal growth factor 
receptor. This is a high-impact fast-moving basic research area with direct 
implications for bettering our understanding of a key cellular process that is 
disrupted in several diseases. The successful applicant will join a 
collaborative team, also involving the laboratories of Professor Philip Woodman 
and Dr Alan Roseman, and will use X-ray crystallography and other structural 
techniques.
The ideal candidate will have (or expect to gain shortly) a PhD in structural 
biology, and will have experience in recombinant protein expression and X-ray 
crystallography.
The post is full time for up to 24 months and can be available immediately.

Salary: £29,541 to £36,298 depending on experience

Closing date :19/03/2013
Reference :LSX-02347
Further particulars and a full description of the project and job 
responsibilities can be found at: 
www.jobs.manchester.ac.uk
Informal enquiries
Informal enquiries can be made to Dr Lydia Tabernero, Lecturer:
Email: lydia.tabern...@manchester.ac.uk
Telephone: 0161 275 7794
The University of Manchester values a diverse workforce and welcomes 
applications from all sections of the community.
Manchester
Protein
Structure
Facility

MIB 1.025
Tel 0161 306 5185
c.l...@manchester.ac.uk

Manchester
Protein
Structure
Facility

MIB 1.025
Tel 0161 306 5185
c.l...@manchester.ac.uk

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[Ian Tickle]

Fred

The relevant bit of code, with the FORMAT statement closed with a ')' and
an END statement added to make it a viable program, is:

  WRITE (*,10)
   10 FORMAT(///,25X,'*',
 . /,25X,'*   *')
  END

For me this compiles and runs without error using gfortran (gcc version
4.7.2).  Maybe you have an old version of gfortran with bugs.  Note that a
statement with continuation lines containing errors usually generates an
error message which specifies only the first line of the statement.  What's
in the rest of the FORMAT statement?

-- Ian


On 6 March 2013 10:37, vellieux  wrote:

> Dear all,
>
> By popular request here is an example of some code where gfortran gives
> run time errors. This is at the very beginning of the program, the first
> write statement where a parenthesis is seen as missing at run time: (the
> first hyphens are not within the Fortran code but there to indicate the
> number of spaces before each character, 6 and nothing more or less).
>
> Also enclosed as "part.f" herewith (as an attachment)
>
> [I must admit that, somehow, when modifying a Fortran program using vim on
> this new box, the number of characters at the beginning of Fortran cards
> seems to reset to 8 when there are 6 blanks to start with, I have no idea
> why this is so.]
>
> Help most welcome, and I'd hate to have to retype every single program...
>
> Ta,
>
> Fred.
>
> --
>
>   ORDER='A'
>   NATM=0
>   DO 5,I=1,3
>  NGRID(2,I)= 9
>  NGRID(3,I)=-9
>  XMIN(I)= .
>  XMAX(I)=-.
>   5  CONTINUE
> C
> C   OPEN INPUT FILE
> C
>   WRITE (*,10)
>10 FORMAT(///,25X,'***',
>  . /,25X,'*   *',
>
>
> --
> Fred. Vellieux (B.Sc., Ph.D., hdr)
> ouvrier de la recherche
> IBS / ELMA
> 41 rue Jules Horowitz
> F-38027 Grenoble Cedex 01
> Tel: +33 438789605
> Fax: +33 438785494
>
>

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[vellieux]

Dear all,

By popular request here is an example of some code where gfortran gives 
run time errors. This is at the very beginning of the program, the first 
write statement where a parenthesis is seen as missing at run time: (the 
first hyphens are not within the Fortran code but there to indicate the 
number of spaces before each character, 6 and nothing more or less).


Also enclosed as "part.f" herewith (as an attachment)

[I must admit that, somehow, when modifying a Fortran program using vim 
on this new box, the number of characters at the beginning of Fortran 
cards seems to reset to 8 when there are 6 blanks to start with, I have 
no idea why this is so.]


Help most welcome, and I'd hate to have to retype every single program...

Ta,

Fred.

--

  ORDER='A'
  NATM=0
  DO 5,I=1,3
 NGRID(2,I)= 9
 NGRID(3,I)=-9
 XMIN(I)= .
 XMAX(I)=-.
  5  CONTINUE
C
C   OPEN INPUT FILE
C
  WRITE (*,10)
   10 FORMAT(///,25X,'*',
 . /,25X,'*   *',

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

  ORDER='A'
  NATM=0
  DO 5,I=1,3
NGRID(2,I)= 9
NGRID(3,I)=-9
XMIN(I)= .
XMAX(I)=-.
  5   CONTINUE
C
C OPEN INPUT FILE
C
  WRITE (*,10)
   10 FORMAT(///,25X,'*',
 . /,25X,'*   *',

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[Ian Clifton]

Hi Fred,

vellieux  writes:


[...]

> I get errors (at run time) of the type:
>
> At line 138 of file program.f (unit = 6, file = 'stdout')
> Fortran runtime error: Missing initial left parenthesis in format
>

[...]

Mmm, that kind of error rings a bell … is the relevant format a string
rather than given in a FORMAT statement? If so, you need round brackets
INSIDE the format string, i.e.

   write (*, '(i5)') 123

rather than

   write (*, 'i5') 123

—this can manifest itself at run‐time, especially if the format is in a
character variable.
-- 
Ian ◎

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[Thomas, Jens]

Hi Fred,


>From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of vellieux 
>[frederic.velli...@ibs.fr]
> When compiling Fortran77 code (these are the flags used for compilation:
> -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double
> -funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the
> libraries on that same compile line)

> I get errors (at run time) of the type:

> At line 138 of file program.f (unit = 6, file = 'stdout')
> Fortran runtime error: Missing initial left parenthesis in format

It might be something to do with fixed vs free format, although I'd have 
thought the -std=legacy should have dealt with that.

You could try adding -ffixed-format and maybe experiment with different values 
for -ffixed-line-length

Things that have bitten me in the past include different backslash 
interpretations, so you could try -fbackslash and also -fd-lines-as-comments if 
there are lines beginning with a D.

If none of that works, maybe you could post the bit of code around the lines 
where you're seeing the error message to see if someone can spot what's 
tripping the compiler up.

Best wishes,

Jens

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[Ian Tickle]

Hi Fred

I regularly compile F77 code with gfortran: I always get lots of warnings
and the occasional error that I didn't get with g77 mainly because gfortran
is much stricter applying the standard (and a good thing too!).  I also
regularly use ifort (which isn't quite as strict as gfortran and
consequently sometimes doesn't spot some real errors).

Maybe if you could post the bit of code it's complaining about (including
say +=5 lines on each side) we could make some specific suggestions.  It's
hard to make suggestions which will cover all eventualities.

Cheers

-- Ian


On 6 March 2013 09:48, vellieux  wrote:

> Hello,
>
> For those who still know the Fortran language and its Fortran 77 variant,
> I used to have a g77 compiler here (Linux box), and now on the new box it's
> no longer g77 but gfortran.
>
> When compiling Fortran77 code (these are the flags used for compilation:
> -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double -funroll-loops
> -ffast-math -fno-second-underscore $1.f , followed by the libraries on that
> same compile line)
>
> I get errors (at run time) of the type:
>
> At line 138 of file program.f (unit = 6, file = 'stdout')
> Fortran runtime error: Missing initial left parenthesis in format
>
> When looking at this code (which compiled perfectly well using g77 - I
> removed the flag "-fno-globals" which doesn't seem to exist any more in
> gfortran) the Fortran code that I see appears to have all parentheses in
> the correct places.
>
> Any idea of what must be done with existing Fortran 77 code in order to
> get it to compile and run with gfortran ? Otherwise any idea which compiler
> should be used to compile Fortran 77 code ?
>
> Thanks in advance,
>
> Fred.
>
> --
> Fred. Vellieux (B.Sc., Ph.D., hdr)
> ouvrier de la recherche
> IBS / ELMA
> 41 rue Jules Horowitz
> F-38027 Grenoble Cedex 01
> Tel: +33 438789605
> Fax: +33 438785494
>

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[Harry Powell]

Hi Fred

If you look very carefully at your Fortran code you will probably   
find a small error/inconsistency that g77 allowed but gfortran picked  
up on or compiled "as written rather than as intended". My move from  
g77 to gfortran when building Mosflm (which is moderately large) was  
pretty painless, but I did find that when I got errors of this type  
the fault was when the code did not adhere to standards.


Generally speaking, gfortran adheres to the current Fortran standards  
more strictly than g77. Recent versions give Mosflm executables that  
are within a few percent of the performance that I get with the Intel  
Fortran ifort compilers (actually, sometimes faster, sometimes  
slower)- I've checked this on both Mac and Linux.


I use gfortran for development, ifort for checking things are still  
okay, and also run an old Linux box with g77 for further checking in  
case I've missed something earlier. My Windows executable of Mosflm  
still uses g77 (the mingw cross-compiler run on OSX).


However, there are persistent reports out there of people who find  
their code runs much faster when compiled with ifort - so I guess  
this is very much code dependent.


I can have a look at your code if it would help.

HTH

On 6 Mar 2013, at Wed6 Mar 09:48, vellieux wrote:


Hello,

For those who still know the Fortran language and its Fortran 77  
variant, I used to have a g77 compiler here (Linux box), and now on  
the new box it's no longer g77 but gfortran.


When compiling Fortran77 code (these are the flags used for  
compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign- 
double -funroll-loops -ffast-math -fno-second-underscore $1.f ,  
followed by the libraries on that same compile line)


I get errors (at run time) of the type:

At line 138 of file program.f (unit = 6, file = 'stdout')
Fortran runtime error: Missing initial left parenthesis in format

When looking at this code (which compiled perfectly well using g77  
- I removed the flag "-fno-globals" which doesn't seem to exist any  
more in gfortran) the Fortran code that I see appears to have all  
parentheses in the correct places.


Any idea of what must be done with existing Fortran 77 code in  
order to get it to compile and run with gfortran ? Otherwise any  
idea which compiler should be used to compile Fortran 77 code ?


Thanks in advance,

Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)

[ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[vellieux]

Hello,

For those who still know the Fortran language and its Fortran 77 
variant, I used to have a g77 compiler here (Linux box), and now on the 
new box it's no longer g77 but gfortran.


When compiling Fortran77 code (these are the flags used for compilation: 
-o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double 
-funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the 
libraries on that same compile line)


I get errors (at run time) of the type:

At line 138 of file program.f (unit = 6, file = 'stdout')
Fortran runtime error: Missing initial left parenthesis in format

When looking at this code (which compiled perfectly well using g77 - I 
removed the flag "-fno-globals" which doesn't seem to exist any more in 
gfortran) the Fortran code that I see appears to have all parentheses in 
the correct places.


Any idea of what must be done with existing Fortran 77 code in order to 
get it to compile and run with gfortran ? Otherwise any idea which 
compiler should be used to compile Fortran 77 code ?


Thanks in advance,

Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494