Frequently Asked Questions
Error: install: Permission denied
Give the correct permissions to file "install" in order to be able to execute it:
$ chmod +x install
Error: nvcc cannot be found. Exiting...
Make sure that the nvcc compiler is in your path:
$ echo $PATH
/usr/local/cuda/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/local/bin
If nvcc is not in your path, you can add it using the following commands:
$ PATH=$PATH:/usr/local/cuda/bin
$ export PATH
Finally, check if the nvcc compiler is now in your path:
$ which nvcc
/usr/local/cuda/bin/nvcc
Error: libcudart.so.7.5: cannot open shared object file: No such file or directory
Make sure that the CUDA libraries are in your $LD_LIBRARY_PATH environment variable.
$ echo $LD_LIBRARY_PATH
/usr/local/cuda/lib64:/usr/local/lib:/opt/local/lib:/opt/local/lib/intel
If CUDA libraries are not in your $LD_LIBRARY_PATH environment variable, you can add them using the following commands:
$ LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64
$ export LD_LIBRARY_PATH
Finally, check if the CUDA libraries are now in your $LD_LIBRARY_PATH environment variable:
$ echo $LD_LIBRARY_PATH
/usr/local/cuda/lib64:/usr/local/lib:/opt/local/lib:/opt/local/lib/intel
Error: Command line argument error: Argument "query". File is not accessible: `../../../../queries/SequenceLength_00000100.txt'
Assuming the installation files are placed on a folder named "blast", the tree structure of the folder "blast" should look like:
blast
|-- database
| |-- env_nr
|-- gpublast
| |-- ncbi_blast_files
| | -- .
| | -- .
| | -- .
| |-- gpu_blastp.c
| |-- .
| |-- .
| |-- .
|-- ncbi-blast-2.2.28+-src/
| |-- c++
| | |-- compilers
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- GCC482-ReleaseMT64
| | | |-- bin
| | | | |-- blastp
| | | | |-- makeblastdb
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- build
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- inc
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- lib
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- status
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | |-- include
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- scripts
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- src
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- config.log
| | |-- configure
| | |-- Makefile
|-- queries
| |-- SequenceLength_00000002.txt
| |-- .
| |-- .
| |-- .
| |-- SequenceLength_00004998.txt
|-- install
|-- README
Calling ./blastp -db ../../../../database/sorted_env_nr -query ../../../../queries/SequenceLength_00000100.txt -gpu t -method 2
that means that there is a folder "queries" inside "blast" directory that contains a file "SequenceLength_00000100.txt" that contains a query.
Make sure that this file exists.
Error: WARNING: Not enough GPU global memory to process volume No. 00 of the database. Continuing without the GPU...
If during execution you get the message:
WARNING: Not enough GPU global memory to process volume No. 00 of the database. Continuing without the GPU...
Consider splitting the input database in volumes with smaller size by using the option "-max_file_size " (e.g. -max_file_sz 500MB).
Consider using fewer GPU blocks and then fewer GPU thread when formatting the database with (e.g. "-gpu_blocks 256" and/or "-gpu_threads 32") to reduce the GPU global memory requirements.
then your GPU does not have enough global memory to carry out the sequence alignment of the
current database volume under the current GPU database configuration. To overcome this problem, you
can reformat the database with "makeblastdb" with a value for "-max_file_sz" smaller than your
previous choice. Another option is to recreate the GPU database by using the options "-method 2" and
smaller values for "-gpu_blocks" and/or "-gpu_threads" than your previous choices (or use smaller
values than 512 and 64 if you let GPU-BLAST create the GPU database with the default values as shown
in the example above).
Error: FATAL: Module nvidia not found. WARNING: There is no available device supporting CUDA. Continuing with the CPU only