No stdout recorded until job finished

[graeme-winter]

19854 gda2      25   5 1311m  85m 5276 R 100.0  0.4   2228:48 refmac5           
 4470 root      20   0  169m  16m 1128 S  2.6  0.1 840:03.77 collectl           
 2588 root      20   0  195m 1180  684 S  0.3  0.0   8:59.41 snmpd              
 3693 root       0 -20 7575m 1.2g 117m S  0.3  4.9  94:53.65 mmfsd              
 4213 sgeadmin  20   0  235m 7308 2540 S  0.3  0.0  77:36.85 sge_execd          
11769 gw56      20   0 17484 1656  980 R  0.3  0.0   0:08.54 top                
    1 root      20   0 25688  568  328 S  0.0  0.0   0:06.34 init      

been running for nearly 2 days... but no stdout so cannot see what it is doing (other than getting stuck)

[wojdyr]

The output will be written out when you kill refmac5.

I see that here it'd be good to get the output as the program is running, but for now it's not high priority, so I'll leave it for later.