I've succeeded to compile h-blast with gcc 4.8.5 and cuda 10.1 on CentOS 8.
I've run the three commands.
$ makeblastdbX -in swissprot.faa -out hblast/swissprot -sort_volumes -max_file_sz 500MB -dbtype prot
Building a new DB, current time: 03/25/2020 18:13:34
New DB name: ./hblast/swissprot
New DB title: ./swissprot.faa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 500000000B
Adding sequences from FASTA; added 473510 sequences in 8.66593 seconds.
Sorting 473510 sequences
Writing to Volume
Done Writing to Database
$ makeGPUDB -db hblast/swissprot
num_volumes = 1
total_offse is 5152
volumne 0
The rest sequence count = 487
The rest sequence group = 0
$ H-BLASTM -module blastp -query land.pep.fa -db hblast/swissprot -out land.swissprot.blast -num_threads 4 -gpu_cards 1 -screen_out check.log
land.pep.fa: 28420 sequences, 10727829 bp => dividing into 1 part . OK
OutputPrefix:land.pep.fa
All done, 0 seconds elapsed
The BLAST search begins!...
Error, please check the srceen output file check.log
$ cat check.log
cudaMemcpyToSymbol error: invalid device symbol
Checking DB volume 0
Please let me know how the problem can be resolved.
Thanks,
Justin
I've succeeded to compile h-blast with gcc 4.8.5 and cuda 10.1 on CentOS 8.
I've run the three commands.
$ makeblastdbX -in swissprot.faa -out hblast/swissprot -sort_volumes -max_file_sz 500MB -dbtype prot
Building a new DB, current time: 03/25/2020 18:13:34
New DB name: ./hblast/swissprot
New DB title: ./swissprot.faa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 500000000B
Adding sequences from FASTA; added 473510 sequences in 8.66593 seconds.
Sorting 473510 sequences
Writing to Volume
Done Writing to Database
$ makeGPUDB -db hblast/swissprot
num_volumes = 1
total_offse is 5152
volumne 0
The rest sequence count = 487
The rest sequence group = 0
$ H-BLASTM -module blastp -query land.pep.fa -db hblast/swissprot -out land.swissprot.blast -num_threads 4 -gpu_cards 1 -screen_out check.log
land.pep.fa: 28420 sequences, 10727829 bp => dividing into 1 part . OK
OutputPrefix:land.pep.fa
All done, 0 seconds elapsed
The BLAST search begins!...
Error, please check the srceen output file check.log
$ cat check.log
cudaMemcpyToSymbol error: invalid device symbol
Checking DB volume 0
Please let me know how the problem can be resolved.
Thanks,
Justin