How can I parallelize on multiple servers?

You can parallelize by chunking. Since ccs v4.0.0, direct chunking via --chunk is possible. For this, the .subreads.bam file must accompanied by a .pbi file. To generate the index subreads.bam.pbi, use pbindex, which can be installed with conda install pbbam.

pbindex movie.subreads.bam

An example workflow, all ccs invocations can run simultaneously:

ccs movie.subreads.bam movie.ccs.1.bam --chunk 1/10 -j <THREADS>
ccs movie.subreads.bam movie.ccs.2.bam --chunk 2/10 -j <THREADS>
...
ccs movie.subreads.bam movie.ccs.10.bam --chunk 10/10 -j <THREADS>

Merge chunks with pbmerge and index with pbindex

pbmerge -o movie.ccs.bam movie.ccs.*.bam
pbindex movie.ccs.bam

or use samtools

samtools merge -@8 movie.ccs.bam movie.ccs.*.bam

THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.