I've been working with a file of almost 2 million compounds. I can export this file as an sd file and it opens fine in Marvin View and can be reimported into Instant JChem (though takes around 6 hours to do so). If I try to import this file into other programmes, only the first ~ 750,000 compounds show properly. The file size of the 750,000 if exported separately is ~ 2 GB. I'm running a i3 540 machine (64 bit) with 16 GB of RAM and wondered if you could help with this ?
what are those other programs? Most likely they use 32-bit long integer values internally as offsets in the file (this was common just a few years ago). An update of that software can provide a fix. Splitting the output into chunks smaller than 2GB can be a solution.
2GB is also the limit for files size on some older file systems (FAT32 often used on Windows until resently, and still often used for USB drives etc.). So if you are transferring the files between disks/computers check that the full file has transferred.
Thanks for both of your comments. I had a feeling that it might be a 32 bit issue. Hasn't involved moving files from one computer to another. Will try updating everything and see what happens.